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Phenotypic Abnormality (PA): Abnormality of the musculature
(show info)
Phenotype Ontology
Like Gene Ontology (GO), phenotypy ontology classifies and organizes gene-mutant/null phenotypic information from the very general at the top to more specific terms in the directed acyclic graph (DAG) by viewing an individual term as a node and its relations to parental terms (allowing for multiple parents) as directed edges. To navigate this hierarchy, we display all parental phenotypic terms to the current phenotypic term of interest ordered by their shortest distances to the current term. Also, only direct children phenotypic terms of the current phenotypic term are listed. Phenotype ontologies we have incorporated are as follows:
- Disease Ontology (DO) Ontology (DO) DO semantically integrates disease and medical vocabularies through extensive cross mapping of DO terms to MeSH, ICD, NCI thesaurus, SNOMED and OMIM.
- Human Phenotype (HP) Ontology (HP) HP captures phenotypic abnormalities that are described in OMIM, along with the corresponding disease-causing genes. It includes three complementary biological concepts: Mode_of_Inheritance (MI), ONset_and_clinical_course (ON), and Phenotypic_Abnormality (PA).
- Mouse Phenotype (MP) Ontology (MP) MP describes phenotypes of the mouse after a specific gene is genetically disrupted. Using it, Mouse Genome Informatics (MGI) provides high-coverate gene-level phenotypes for the mouse.
- Worm Phenotype (WP) Ontology (WP) WP classifies and organizes phenotype descriptions for C. elegans and other nematodes. Using it, WormBase provides primary resource for phenotype annotations for C. elegans.
- Yeast Phenotype (YP) Ontology (YP) Based on YP which is the major contributor to the Ascomycete phenotype ontology, Saccharomyces Genome Database (SGD) provides single mutant phenotypes for every gene in the yeast genome.
- Fly Phenotype (FP) Ontology (FP) FP refers to FlyBase controlled vocabulary. Specifically, a structured controlled vocabulary is used for the annotation of alleles (for their mutagen etc) in FlyBase.
- Fly Anatomy (FA) Ontology (FA) FA is a structured controlled vocabulary of the anatomy of Drosophila melanogaster, used for the description of phenotypes and where a gene is expressed.
- Zebrafish Anatomy (ZA) Ontology (ZA) ZA displays anatomical terms of the zebrafish using standard anatomical nomenclature, together with affected genes.
- Xenopus Anatomy (XA) Ontology (XA) XA represents the lineage of tissues and the timing of development for frogs (Xenopus laevis and Xenopus tropicalis). It is used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes.
- Arabidopsis Plant Ontology (AP) Ontology (AP) As a major contributor to Plant Ontology which describes plant anatomical and morphological structures (AN) and growth and developmental stages (DE), the Arabidopsis Information Resource (TAIR) provides arabidopsis plant ontology annotations for the model higher plant Arabidopsis thaliana.
- Enzyme Commission (EC) Ontology (EC) Each enzyme is allocated a four-digit EC number, the first three digits of which define the reaction catalysed and the fourth of which is a unique identifier (serial number). Each enzyme is also assigned a systematic name that uniquely defines the reaction catalysed.
- DrugBank ATC (DB) Ontology (DB) In the Anatomical Therapeutic Chemical (ATC) classification system, drugs are classified in groups at five different levels according to the organ or system (1st level, anatomical main group) on which they act and their therapeutic (2nd level, therapeutic subgroup), pharmacological (3rd level, pharmacological subgroup) and chemical properties (4th level, chemical subgroup; 5th level, chemical substance). Only drugs in DrugBank are considered.
- UniProtKB KeyWords (KW) Ontology (KW) Keywords in UniProtKB are controlled vocabulary, providing a summary of the entry content and are used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here). Each keyword is attributed manually to UniProtKB/Swiss-Prot entries and automatically to UniProtKB/TrEMBL entries (according to specific annotation rules).
- UniProtKB UniPathway (UP) Ontology (UP) UP is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as controlled vocabulary for pathway annotation in UniProtKB.
Structural Domain Phenotype Ontology and its Annotations
Structural Classification of Proteins (SCOP) classifies evolutionary-related domains into Superfamily level and Family level. Using the phenotype ontologies above, we have generated the domain-centric phenotype annotations, and further identified those phenotype terms which are the most informative to annotate SCOP domains. Promisingly, domain-centric phenotypic annotations can serve as an alternative starting point to explore genotype-phenotype relationships. We provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Structural Domain Disease Ontology (DO) Ontology (SDDO) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DO.txt, and the corresponding ontology:SDDO.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Human Phenotype (HP) Ontology (SDHP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2HP.txt, and the corresponding ontology:SDHP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Mouse Phenotype (MP) Ontology (SDMP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2MP.txt, and the corresponding ontology:SDMP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Worm Phenotype (WP) Ontology (SDWP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2WP.txt, and the corresponding ontology:SDWP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Yeast Phenotype (YP) Ontology (SDYP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2YP.txt, and the corresponding ontology:SDYP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Phenotype (FP) Ontology (SDFP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FP.txt, and the corresponding ontology:SDFP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Fly Anatomy (FA) Ontology (SDFA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2FA.txt, and the corresponding ontology:SDFA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Zebrafish Anatomy (ZA) Ontology (SDZA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2ZA.txt, and the corresponding ontology:SDZA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Xenopus Anatomy (XA) Ontology (SDXA) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2XA.txt, and the corresponding ontology:SDXA.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Arabidopsis Plant Ontology (AP) Ontology (SDAP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2AP.txt, and the corresponding ontology:SDAP.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain Enzyme Commission (EC) Ontology (SDEC) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2EC.txt, and the corresponding ontology:SDEC.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain DrugBank ATC (DB) Ontology (SDDB) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2DB.txt, and the corresponding ontology:SDDB.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB KeyWords (KW) Ontology (SDKW) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2KW.txt, and the corresponding ontology:SDKW.txt) and mysql tables (Domain2PO.sql.gz).
- Structural Domain UniProtKB UniPathway (UP) Ontology (SDUP) and its Annotations: For details, please visit Document: PO annotation for SCOP domains, wherein Data Availability contains parsable flat files (the annotation:Domain2UP.txt, and the corresponding ontology:SDUP.txt) and mysql tables (Domain2PO.sql.gz).
Supra-domain Phenotype Ontology and its Annotations
Although domain-centric annotations hold great promise in describing phenotypic nature of independent domains, most domains themselves may not just work alone. In multi-domain proteins, they may be combined together to form distinct domain architectures. The recombination of the existing domains is considered as one of major driving forces for phenotypic diversificaation. As an extension, we have also generated supra-domain phenotype ontology and its annotations. Compared to domain-centric phenotype ontology and annotations (SCOP domains at the Superfamily level and Family level), this version focuses on supra-domains and individual SCOP domains ONLY at the Superfamily level. Besides, in terms of individual superfamilies, their annotations from the domain-centric version may be different from those from supra-domains version. Depending on your focus, the former should be used for the consideration of both the Superfamily level and Family level, otherwise the latter should be used if you are interested in domain combinations. Also, we provide several relevant files for the download, including the annotation and the corresponding ontology for each phenotype ontology.
- Supra-domain Domain Disease Ontology (DO) Ontology (SPDO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DO.txt, and the corresponding ontology:SPDO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Human Phenotype (HP) Ontology (SPHO) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2HP.txt, and the corresponding ontology:SPHO.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Mouse Phenotype (MP) Ontology (SPMP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2MP.txt, and the corresponding ontology:SPMP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Worm Phenotype (WP) Ontology (SPWP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2WP.txt, and the corresponding ontology:SPWP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Yeast Phenotype (YP) Ontology (SPYP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2YP.txt, and the corresponding ontology:SPYP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Phenotype (FP) Ontology (SPFP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FP.txt, and the corresponding ontology:SPFP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Fly Anatomy (FA) Ontology (SPFA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2FA.txt, and the corresponding ontology:SPFA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Zebrafish Anatomy (ZA) Ontology (SPZA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2ZA.txt, and the corresponding ontology:SPZA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Xenopus Anatomy (XA) Ontology (SPXA) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2XA.txt, and the corresponding ontology:SPXA.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Arabidopsis Plant Ontology (AP) Ontology (SPAP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2AP.txt, and the corresponding ontology:SPAP.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain Enzyme Commission (EC) Ontology (SPEC) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2EC.txt, and the corresponding ontology:SPEC.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain DrugBank ATC (DB) Ontology (SPDB) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2DB.txt, and the corresponding ontology:SPDB.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB KeyWords (KW) Ontology (SPKW) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2KW.txt, and the corresponding ontology:SPKW.txt) and mysql tables (SP2PO.sql.gz).
- Supra-domain Domain UniProtKB UniPathway (UP) Ontology (SPUP) and its Annotations: For details, please visit Document: PO annotation for Supra-domains, wherein Data Availability contains parsable flat files (the annotation:SP2UP.txt, and the corresponding ontology:SPUP.txt) and mysql tables (SP2PO.sql.gz).
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Root: HP Hierarchy (human phenotype with 3 sub-ontologies PA, MI, ON)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Superfamily(show details)
Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Family(show details)
Family domains annotated to this HP term (SDHP level: Least Informative)
Highlighted in gray are those with FDR_all>0.001
SCOP term | FDR (all) | Annotation (direct or inherited) |
CCCH zinc finger | 0 | DIRECT |
Proteasome subunits | 0 | DIRECT |
a tRNA synthase domain | 0 | DIRECT |
Amylase, catalytic domain | 0 | DIRECT |
Myotubularin-like phosphatases | 0 | DIRECT |
Double-stranded RNA-binding domain (dsRBD) | 0 | DIRECT |
Ferredoxin domains from multidomain proteins | 0 | DIRECT |
Filamin repeat (rod domain) | 0 | DIRECT |
Protein serine/threonine phosphatase | 0 | DIRECT |
Multidrug efflux transporter AcrB transmembrane domain | 0 | DIRECT |
BC N-terminal domain-like | 0 | DIRECT |
N-acetyl transferase, NAT | 0 | DIRECT |
Serum paraoxonase/arylesterase 1, PON1 | 0 | DIRECT |
alpha-Amylases, C-terminal beta-sheet domain | 0 | DIRECT |
Lamin A/C globular tail domain | 0 | DIRECT |
Glycosyl transferases group 1 | 0 | DIRECT |
Cytochrome b5 | 0 | DIRECT |
SNARE fusion complex | 0 | DIRECT |
Phosphate binding protein-like | 0 | DIRECT |
beta-glycanases | 0 | DIRECT |
Troponin T | 0 | DIRECT |
Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A | 0 | DIRECT |
PP2C-like | 0 | DIRECT |
Smc hinge domain | 0 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase Pyr module | 0 | DIRECT |
Choline/Carnitine O-acyltransferase | 0 | DIRECT |
FKBP immunophilin/proline isomerase | 0 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase PP module | 0 | DIRECT |
GABA-aminotransferase-like | 0 | DIRECT |
Aminomethyltransferase beta-barrel domain | 0 | DIRECT |
Hect, E3 ligase catalytic domain | 0 | DIRECT |
Ribonuclease PH domain 1-like | 0 | DIRECT |
C5 cytosine-specific DNA methylase, DCM | 0 | DIRECT |
Ubiquitin carboxyl-terminal hydrolase, UCH | 0 | DIRECT |
Biotin dependent carboxylase carboxyltransferase domain | 0 | DIRECT |
Exostosin | 0 | DIRECT |
Histone lysine methyltransferases | 0 | DIRECT |
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
Inositol polyphosphate 5-phosphatase (IPP5) | 0 | DIRECT |
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain | 0 | DIRECT |
BC C-terminal domain-like | 0 | DIRECT |
FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | DIRECT |
UBA domain | 0 | DIRECT |
Ribonuclease PH domain 2-like | 0 | DIRECT |
Anticodon-binding domain | 0 | DIRECT |
DNA polymerase I | 0 | DIRECT |
Aminomethyltransferase folate-binding domain | 0 | DIRECT |
IF2B-like | 0 | DIRECT |
BC ATP-binding domain-like | 0 | DIRECT |
Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.0001752 | DIRECT |
Extended AAA-ATPase domain | 0.001226 | INHERITED FROM: Spasticity |
G proteins | 0.001836 | INHERITED FROM: Aplasia/Hypoplasia of the abdominal wall musculature |
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.007017 | INHERITED FROM: Abnormality of the musculature of the limbs |
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.0115 | INHERITED FROM: Abnormal muscle tone |
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.01862 | INHERITED FROM: Muscular hypotonia |
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.01862 | INHERITED FROM: Muscular hypotonia |
Biotinyl/lipoyl-carrier proteins and domains | 0.01862 | INHERITED FROM: Muscular hypotonia |
Laminin-type module | 0.01877 | INHERITED FROM: Muscle fiber atrophy || EMG abnormality |
Neurotransmitter-gated ion-channel transmembrane pore | 0.02536 | INHERITED FROM: Neck flexor weakness || Neck muscle weakness || Abnormality of the musculature of the hand || Triceps weakness || Pelvic girdle muscle weakness || Fatigable weakness of skeletal muscles || Hand muscle weakness || Abnormality of jaw muscles || Hip flexor weakness || Fatigable weakness of neck muscles || Shoulder girdle muscle weakness || Fatigable weakness of respiratory muscles || Limb-girdle muscle weakness || Amyoplasia || Weakness of the intrinsic hand muscles || Proximal muscle weakness in upper limbs || EMG: impaired neuromuscular transmission || Ankle weakness || Easy fatigability || Weakness of long finger extensor muscles || EMG: decremental response of compound muscle action potential to repetitive nerve stimulation || Aplasia of the musculature || Aplasia/Hypoplasia involving the skeletal musculature |
Nicotinic receptor ligand binding domain-like | 0.02536 | INHERITED FROM: Neck flexor weakness || Neck muscle weakness || Abnormality of the musculature of the hand || Triceps weakness || Pelvic girdle muscle weakness || Fatigable weakness of skeletal muscles || Hand muscle weakness || Abnormality of jaw muscles || Hip flexor weakness || Fatigable weakness of neck muscles || Shoulder girdle muscle weakness || Fatigable weakness of respiratory muscles || Limb-girdle muscle weakness || Amyoplasia || Weakness of the intrinsic hand muscles || Proximal muscle weakness in upper limbs || EMG: impaired neuromuscular transmission || Ankle weakness || Easy fatigability || Weakness of long finger extensor muscles || EMG: decremental response of compound muscle action potential to repetitive nerve stimulation || Aplasia of the musculature || Aplasia/Hypoplasia involving the skeletal musculature |
Tropomyosin | 0.0295 | INHERITED FROM: Neck muscle weakness || Muscle fiber inclusion bodies || Knee flexion contracture || Congenital contracture || Abnormality of the shoulder girdle musculature || Scapular winging || Contractures of the joints of the lower limbs || Hip contracture || Elbow flexion contracture |
Spectrin repeat | 0.06928 | INHERITED FROM: Achilles tendon contracture || Muscular dystrophy || Decreased cervical spine flexion due to contractures of posterior cervical muscles |
ValRS/IleRS/LeuRS editing domain | 0.0736 | INHERITED FROM: Generalized hypotonia |
ARID domain | 0.0736 | INHERITED FROM: Abnormality of the diaphragm |
PHD domain | 0.08044 | INHERITED FROM: Abnormality of the diaphragm || Muscular hypotonia |
Calponin-homology domain, CH-domain | 0.08534 | INHERITED FROM: Scapular winging || Contractures of the joints of the lower limbs || Decreased cervical spine flexion due to contractures of posterior cervical muscles || Abnormality of the musculature of the lower limbs |
HMG-box | 0.08534 | INHERITED FROM: Abnormality of the diaphragm || Congenital diaphragmatic hernia |
Elongation factors | 0.09083 | INHERITED FROM: Spasticity |
DNA gyrase/MutL, second domain | 0.114 | INHERITED FROM: Flexion contracture |
Clathrin adaptor core protein | 0.114 | INHERITED FROM: Difficulty walking |
DNA gyrase/MutL, N-terminal domain | 0.114 | INHERITED FROM: Flexion contracture |
Anticodon-binding domain of Class II aaRS | 0.1304 | INHERITED FROM: Abnormality of the musculature of the limbs |
FHA domain | 0.179 | INHERITED FROM: Skeletal muscle atrophy |
Myosin rod fragments | 0.179 | INHERITED FROM: Lower limb muscle weakness || Abnormality of the shoulder girdle musculature || Scapular winging |
VWC domain | 0.1862 | INHERITED FROM: Aplasia/Hypoplasia of the abdominal wall musculature || Abnormal morphology of the abdominal musculature |
Kelch motif | 0.2002 | INHERITED FROM: Muscle fiber inclusion bodies || Type 1 muscle fiber predominance || Nemaline bodies || Weakness of facial musculature || Muscle fiber cytoplasmatic inclusion bodies |
LIM domain | 0.4022 | INHERITED FROM: Myopathy || Abnormality of the musculature of the lower limbs |
MIR domain | 0.4208 | INHERITED FROM: Fatigable weakness || Proximal amyotrophy || Muscle hypertrophy of the lower extremities || Muscular dystrophy || Proximal muscle weakness || Abnormality of the musculature of the upper limbs || Axial muscle weakness || Difficulty climbing stairs || Generalized muscle weakness || Limb-girdle muscle weakness || Skeletal muscle hypertrophy || Infantile muscular hypotonia || Abnormality of the calf musculature || Calf muscle hypertrophy || Multiple joint contractures || Abnormality of the musculature of the lower limbs |
Canonical RBD | 0.4622 | INHERITED FROM: Fatigable weakness of bulbar muscles || Fatigable weakness of swallowing muscles || Rimmed vacuoles || Fatigable weakness of respiratory muscles |
GLA-domain | 0.6828 | INHERITED FROM: Intramuscular hematoma |
Integrin A (or I) domain | 0.7902 | INHERITED FROM: Muscle fiber necrosis || Reduced muscle collagen VI || Contractures of the joints of the upper limbs || Progressive proximal muscle weakness || Proximal amyotrophy || Flexion contracture of finger || Torticollis || Abnormal morphology of the musculature of the neck || Muscular dystrophy || Frequent falls || Camptodactyly || Abnormality of skeletal muscle fiber size || Interphalangeal joint contracture of finger || Ankle flexion contracture || Progressive muscle weakness || Increased variability in muscle fiber diameter || Increased endomysial connective tissue || Diaphragmatic weakness || Congenital muscular dystrophy |
Eukaryotic proteases | 1 | INHERITED FROM: Intramuscular hematoma |
Intermediate filament protein, coiled coil region | 1 | INHERITED FROM: Fatigable weakness |
SCOP term | FDR (all) | Annotation (direct or inherited) |
CCCH zinc finger | 0 | Direct |
Proteasome subunits | 0 | Direct |
a tRNA synthase domain | 0 | Direct |
Amylase, catalytic domain | 0 | Direct |
Myotubularin-like phosphatases | 0 | Direct |
Double-stranded RNA-binding domain (dsRBD) | 0 | Direct |
Ferredoxin domains from multidomain proteins | 0 | Direct |
Filamin repeat (rod domain) | 0 | Direct |
Protein serine/threonine phosphatase | 0 | Direct |
Multidrug efflux transporter AcrB transmembrane domain | 0 | Direct |
BC N-terminal domain-like | 0 | Direct |
N-acetyl transferase, NAT | 0 | Direct |
Serum paraoxonase/arylesterase 1, PON1 | 0 | Direct |
alpha-Amylases, C-terminal beta-sheet domain | 0 | Direct |
Lamin A/C globular tail domain | 0 | Direct |
Glycosyl transferases group 1 | 0 | Direct |
Cytochrome b5 | 0 | Direct |
SNARE fusion complex | 0 | Direct |
Phosphate binding protein-like | 0 | Direct |
beta-glycanases | 0 | Direct |
Troponin T | 0 | Direct |
Association domain of calcium/calmodulin-dependent protein kinase type II alpha subunit, CAMK2A | 0 | Direct |
PP2C-like | 0 | Direct |
Smc hinge domain | 0 | Direct |
Branched-chain alpha-keto acid dehydrogenase Pyr module | 0 | Direct |
Choline/Carnitine O-acyltransferase | 0 | Direct |
FKBP immunophilin/proline isomerase | 0 | Direct |
Branched-chain alpha-keto acid dehydrogenase PP module | 0 | Direct |
GABA-aminotransferase-like | 0 | Direct |
Aminomethyltransferase beta-barrel domain | 0 | Direct |
Hect, E3 ligase catalytic domain | 0 | Direct |
Ribonuclease PH domain 1-like | 0 | Direct |
C5 cytosine-specific DNA methylase, DCM | 0 | Direct |
Ubiquitin carboxyl-terminal hydrolase, UCH | 0 | Direct |
Biotin dependent carboxylase carboxyltransferase domain | 0 | Direct |
Exostosin | 0 | Direct |
Histone lysine methyltransferases | 0 | Direct |
EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
Inositol polyphosphate 5-phosphatase (IPP5) | 0 | Direct |
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain | 0 | Direct |
BC C-terminal domain-like | 0 | Direct |
FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | Direct |
UBA domain | 0 | Direct |
Ribonuclease PH domain 2-like | 0 | Direct |
Anticodon-binding domain | 0 | Direct |
DNA polymerase I | 0 | Direct |
Aminomethyltransferase folate-binding domain | 0 | Direct |
IF2B-like | 0 | Direct |
BC ATP-binding domain-like | 0 | Direct |
Class I aminoacyl-tRNA synthetases (RS), catalytic domain | 0.0001752 | Direct |
Extended AAA-ATPase domain | 0.001226 | Inherited |
G proteins | 0.001836 | Inherited |
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain | 0.007017 | Inherited |
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.0115 | Inherited |
Medium chain acyl-CoA dehydrogenase-like, C-terminal domain | 0.01862 | Inherited |
Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains | 0.01862 | Inherited |
Biotinyl/lipoyl-carrier proteins and domains | 0.01862 | Inherited |
Laminin-type module | 0.01877 | Inherited |
Neurotransmitter-gated ion-channel transmembrane pore | 0.02536 | Inherited |
Nicotinic receptor ligand binding domain-like | 0.02536 | Inherited |
Tropomyosin | 0.0295 | Inherited |
Spectrin repeat | 0.06928 | Inherited |
ValRS/IleRS/LeuRS editing domain | 0.0736 | Inherited |
ARID domain | 0.0736 | Inherited |
PHD domain | 0.08044 | Inherited |
Calponin-homology domain, CH-domain | 0.08534 | Inherited |
HMG-box | 0.08534 | Inherited |
Elongation factors | 0.09083 | Inherited |
DNA gyrase/MutL, second domain | 0.114 | Inherited |
Clathrin adaptor core protein | 0.114 | Inherited |
DNA gyrase/MutL, N-terminal domain | 0.114 | Inherited |
Anticodon-binding domain of Class II aaRS | 0.1304 | Inherited |
FHA domain | 0.179 | Inherited |
Myosin rod fragments | 0.179 | Inherited |
VWC domain | 0.1862 | Inherited |
Kelch motif | 0.2002 | Inherited |
LIM domain | 0.4022 | Inherited |
MIR domain | 0.4208 | Inherited |
Canonical RBD | 0.4622 | Inherited |
GLA-domain | 0.6828 | Inherited |
Integrin A (or I) domain | 0.7902 | Inherited |
Eukaryotic proteases | 1 | Inherited |
Intermediate filament protein, coiled coil region | 1 | Inherited |
Plot distribution on phylogenetic tree for Superfamily and/or Family domains annotated by this phenotype term
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A presence/absence matrix is generated using protein domain
architecture data for all genomes in SUPERFAMILY. The PAUP
software is used to produce a single, large tree topology using
heuristic parsimony methods. Genome combinations, or specific clades, can be displayed as
if individual trees had been produced. However, this data is extracted from the single
large tree. This produces a higher quality topology than if the trees had been produced
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Jump to [ Top · Phenotype Hierarchy · Superfamily · Family · Supra-domain ]
Supra-domain (including individual superfamily)
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Supra-domains annotated to this HP term (SPHO level: Least Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
53098,56672 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases | 0 | DIRECT |
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases | 0 | DIRECT |
56059,51246 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0 | DIRECT |
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | DIRECT |
103025,101790 103025 - Folate-binding domain 101790 - Aminomethyltransferase beta-barrel domain | 0 | DIRECT |
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger | 0 | DIRECT |
50447,54980 50447 - Translation proteins 54980 - EF-G C-terminal domain-like | 0 | DIRECT |
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | DIRECT |
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | DIRECT |
54211,55666 54211 - Ribosomal protein S5 domain 2-like 55666 - Ribonuclease PH domain 2-like | 0 | DIRECT |
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0 | DIRECT |
57850,57845 57850 - RING/U-box 57845 - B-box zinc-binding domain | 0 | DIRECT |
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like | 0 | DIRECT |
51905,55424 51905 - FAD/NAD(P)-binding domain 55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | DIRECT |
54928,90209 54928 - RNA-binding domain, RBD 90209 - Ran binding protein zinc finger-like | 0 | DIRECT |
53822,53850 53822 - Periplasmic binding protein-like I 53850 - Periplasmic binding protein-like II | 0 | DIRECT |
47060,55681 47060 - S15/NS1 RNA-binding domain 55681 - Class II aaRS and biotin synthetases | 0 | DIRECT |
52518,52922 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52922 - TK C-terminal domain-like | 0 | DIRECT |
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases | 0 | DIRECT |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.01978 | INHERITED FROM: Weakness of muscles of respiration || Fatigable weakness of respiratory muscles || Distal muscle weakness || Abnormal muscle fiber morphology || Abnormality of muscle size || Fatigable weakness of bulbar muscles || Rimmed vacuoles || Skeletal muscle atrophy || Fatigable weakness of swallowing muscles |
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.0279 | INHERITED FROM: Aplasia of the musculature || Easy fatigability || Shoulder girdle muscle weakness || Fatigable weakness of respiratory muscles || Abnormality of the musculature of the hand || Amyoplasia || Hand muscle weakness || Weakness of the intrinsic hand muscles || Aplasia/Hypoplasia involving the skeletal musculature || Abnormality of the shoulder girdle musculature || Abnormality of jaw muscles || Fatigable weakness of neck muscles || Weakness of long finger extensor muscles || Pelvic girdle muscle weakness || Neck muscle weakness || Neck flexor weakness || EMG: impaired neuromuscular transmission || Proximal muscle weakness in upper limbs || Ankle weakness || EMG: decremental response of compound muscle action potential to repetitive nerve stimulation || Triceps weakness || Hip flexor weakness || Fatigable weakness of skeletal muscles |
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin | 0.04867 | INHERITED FROM: Arthrogryposis multiplex congenita |
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat | 0.05123 | INHERITED FROM: Contractures of the joints of the lower limbs || Achilles tendon contracture || Abnormality of the musculature of the lower limbs || Decreased cervical spine flexion due to contractures of posterior cervical muscles || Muscular dystrophy |
50677,52374 50677 - ValRS/IleRS/LeuRS editing domain 52374 - Nucleotidylyl transferase | 0.07556 | INHERITED FROM: Generalized hypotonia |
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins | 0.0947 | INHERITED FROM: Spasticity |
55874,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 domain 2-like | 0.1173 | INHERITED FROM: Flexion contracture |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.2455 | INHERITED FROM: Interphalangeal joint contracture of finger || Contractures of the joints of the upper limbs |
81296,81296 81296 - E set domains 81296 - E set domains | 0.2677 | INHERITED FROM: Abnormality of the musculature of the upper limbs |
48371,48371 48371 - ARM repeat 48371 - ARM repeat | 0.2957 | INHERITED FROM: Hypomimic face |
53300,53300 53300 - vWA-like 53300 - vWA-like | 0.3694 | INHERITED FROM: Interphalangeal joint contracture of finger || EMG: myopathic abnormalities || Diaphragmatic weakness || Weakness of muscles of respiration || Congenital muscular torticollis || Distal muscle weakness || Torticollis || Abnormal muscle fiber morphology || Progressive muscle weakness || EMG abnormality || Contractures of the joints of the upper limbs || Contractures of the joints of the lower limbs || Respiratory insufficiency due to muscle weakness || Proximal muscle weakness || Facial palsy || Multiple joint contractures || Abnormality of skeletal muscle fiber size || Joint contracture of the hand || Limb-girdle muscle weakness || Reduced muscle collagen VI || Generalized muscle weakness || Neonatal hypotonia || Frequent falls || Generalized amyotrophy || Weakness of facial musculature || Camptodactyly || Abnormal muscle fiber protein expression || Increased variability in muscle fiber diameter || Increased endomysial connective tissue || Abnormal morphology of the musculature of the neck || Congenital muscular dystrophy || Myopathy || Ankle flexion contracture || Camptodactyly of finger || Knee flexion contracture || Muscle fiber necrosis || Flexion contracture of finger || Progressive proximal muscle weakness || Proximal amyotrophy || Type 1 muscle fiber predominance || Abnormality of facial musculature || Elbow flexion contracture || Flexion contracture of digit || Muscular dystrophy |
50729,50729 50729 - PH domain-like 50729 - PH domain-like | 0.4282 | INHERITED FROM: Interphalangeal joint contracture of finger || Camptodactyly of finger |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.5271 | INHERITED FROM: Abnormality of the musculature of the lower limbs |
Supra-domain (Duplex) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
53098,56672 53098 - Ribonuclease H-like 56672 - DNA/RNA polymerases | 0 | Direct |
50249,55681 50249 - Nucleic acid-binding proteins 55681 - Class II aaRS and biotin synthetases | 0 | Direct |
56059,51246 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0 | Direct |
47005,52777 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | Direct |
103025,101790 103025 - Folate-binding domain 101790 - Aminomethyltransferase beta-barrel domain | 0 | Direct |
57903,57903 57903 - FYVE/PHD zinc finger 57903 - FYVE/PHD zinc finger | 0 | Direct |
50447,54980 50447 - Translation proteins 54980 - EF-G C-terminal domain-like | 0 | Direct |
50447,50465 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
49265,48726 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | Direct |
51230,47005 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 0 | Direct |
54211,55666 54211 - Ribosomal protein S5 domain 2-like 55666 - Ribonuclease PH domain 2-like | 0 | Direct |
52518,52518 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52518 - Thiamin diphosphate-binding fold (THDP-binding) | 0 | Direct |
57850,57845 57850 - RING/U-box 57845 - B-box zinc-binding domain | 0 | Direct |
54768,54768 54768 - dsRNA-binding domain-like 54768 - dsRNA-binding domain-like | 0 | Direct |
51905,55424 51905 - FAD/NAD(P)-binding domain 55424 - FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 0 | Direct |
54928,90209 54928 - RNA-binding domain, RBD 90209 - Ran binding protein zinc finger-like | 0 | Direct |
53822,53850 53822 - Periplasmic binding protein-like I 53850 - Periplasmic binding protein-like II | 0 | Direct |
47060,55681 47060 - S15/NS1 RNA-binding domain 55681 - Class II aaRS and biotin synthetases | 0 | Direct |
52518,52922 52518 - Thiamin diphosphate-binding fold (THDP-binding) 52922 - TK C-terminal domain-like | 0 | Direct |
52777,52777 52777 - CoA-dependent acyltransferases 52777 - CoA-dependent acyltransferases | 0 | Direct |
54928,54928 54928 - RNA-binding domain, RBD 54928 - RNA-binding domain, RBD | 0.01978 | Inherited |
63712,90112 63712 - Nicotinic receptor ligand binding domain-like 90112 - Neurotransmitter-gated ion-channel transmembrane pore | 0.0279 | Inherited |
49899,57196 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin | 0.04867 | Inherited |
46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat | 0.05123 | Inherited |
50677,52374 50677 - ValRS/IleRS/LeuRS editing domain 52374 - Nucleotidylyl transferase | 0.07556 | Inherited |
52540,50447 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins | 0.0947 | Inherited |
55874,54211 55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 54211 - Ribosomal protein S5 domain 2-like | 0.1173 | Inherited |
57196,57196 57196 - EGF/Laminin 57196 - EGF/Laminin | 0.2455 | Inherited |
81296,81296 81296 - E set domains 81296 - E set domains | 0.2677 | Inherited |
48371,48371 48371 - ARM repeat 48371 - ARM repeat | 0.2957 | Inherited |
53300,53300 53300 - vWA-like 53300 - vWA-like | 0.3694 | Inherited |
50729,50729 50729 - PH domain-like 50729 - PH domain-like | 0.4282 | Inherited |
57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.5271 | Inherited |
(show details)
Supra-domains annotated to this HP term (SPHO level: Least Informative)
Highlighted in gray are those with FDR>0.001
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | DIRECT |
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | DIRECT |
52440,56059,51246 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0 | DIRECT |
51230,47005,52777 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | DIRECT |
49899,49899,57196 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin | 0 | DIRECT |
52540,50447,54980 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 54980 - EF-G C-terminal domain-like | 0 | DIRECT |
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat | 0.02033 | INHERITED FROM: Contractures involving the joints of the feet || Contractures of the joints of the lower limbs || Achilles tendon contracture || Abnormality of the musculature of the lower limbs || Decreased cervical spine flexion due to contractures of posterior cervical muscles || Muscular dystrophy |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.1354 | INHERITED FROM: Myopathy || Abnormality of the musculature of the lower limbs |
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains | 0.2677 | INHERITED FROM: Abnormality of the musculature of the upper limbs |
Supra-domain (Triple) in N- to C-terminal order |
FDR (all) |
Annotation (direct or inherited) |
48726,49265,48726 48726 - Immunoglobulin 49265 - Fibronectin type III 48726 - Immunoglobulin | 0 | Direct |
52540,50447,50465 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 50465 - EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 0 | Direct |
52440,56059,51246 52440 - PreATP-grasp domain 56059 - Glutathione synthetase ATP-binding domain-like 51246 - Rudiment single hybrid motif | 0 | Direct |
51230,47005,52777 51230 - Single hybrid motif 47005 - Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 52777 - CoA-dependent acyltransferases | 0 | Direct |
49899,49899,57196 49899 - Concanavalin A-like lectins/glucanases 49899 - Concanavalin A-like lectins/glucanases 57196 - EGF/Laminin | 0 | Direct |
52540,50447,54980 52540 - P-loop containing nucleoside triphosphate hydrolases 50447 - Translation proteins 54980 - EF-G C-terminal domain-like | 0 | Direct |
46966,46966,46966 46966 - Spectrin repeat 46966 - Spectrin repeat 46966 - Spectrin repeat | 0.02033 | Inherited |
57716,57716,57716 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) 57716 - Glucocorticoid receptor-like (DNA-binding domain) | 0.1354 | Inherited |
81296,81296,81296 81296 - E set domains 81296 - E set domains 81296 - E set domains | 0.2677 | Inherited |
Plot distribution on phylogenetic tree for Supra-domains (Single/Individual) annotated by this phenotype term
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A presence/absence matrix is generated using protein domains and supradomains
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