OTUD7A
Basic information
Region (hg38): 15:31475397-31870789
Previous symbols: [ "C15orf16", "OTUD7" ]
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (31 variants)
- not provided (9 variants)
- OTUD7A-related condition (4 variants)
- Specific learning disability (1 variants)
- Non-syndromic intellectual disability (1 variants)
- Language disorder;Severe global developmental delay;Epileptic encephalopathy (1 variants)
- Neurodevelopmental disorder (1 variants)
- See cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OTUD7A gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | |||||
missense | 32 | 35 | ||||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region ? | 0 | |||||
non coding ? | 1 | |||||
Total | 2 | 1 | 38 | 2 | 5 |
Variants in OTUD7A
This is a list of pathogenic ClinVar variants found in the OTUD7A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-31483422-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
15-31483428-G-C | not specified | Uncertain significance (Apr 08, 2023) | ||
15-31483449-C-G | See cases | Uncertain significance (Nov 04, 2020) | ||
15-31483457-C-G | not specified | Uncertain significance (Apr 13, 2022) | ||
15-31483468-C-CGCGTCG | Uncertain significance (Apr 26, 2022) | |||
15-31483512-A-G | not specified | Uncertain significance (Jun 12, 2023) | ||
15-31483519-G-C | Likely benign (Feb 01, 2024) | |||
15-31483548-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
15-31483557-T-C | not specified | Likely benign (Apr 12, 2023) | ||
15-31483600-C-T | OTUD7A-related disorder | Benign (Jul 12, 2019) | ||
15-31483642-C-G | Likely benign (Aug 01, 2022) | |||
15-31483646-C-A | not specified | Uncertain significance (Jul 13, 2022) | ||
15-31483730-T-TCGTCCCGCGCGCCC | OTUD7A-related disorder | Uncertain significance (Mar 30, 2023) | ||
15-31483749-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
15-31483779-G-A | not specified | Uncertain significance (Feb 11, 2022) | ||
15-31483781-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
15-31483788-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
15-31483801-C-G | OTUD7A-related disorder | Benign (Jun 06, 2022) | ||
15-31483809-C-T | not specified | Uncertain significance (May 18, 2023) | ||
15-31483818-T-C | OTUD7A-related disorder | Benign (Mar 12, 2021) | ||
15-31483829-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
15-31483839-C-A | not specified | Uncertain significance (Oct 16, 2023) | ||
15-31483839-C-G | not specified | Uncertain significance (Aug 16, 2022) | ||
15-31483861-C-A | OTUD7A-related disorder | Benign/Likely benign (Apr 01, 2022) | ||
15-31483895-G-C | not specified | Uncertain significance (Jan 10, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
OTUD7A | protein_coding | protein_coding | ENST00000307050 | 11 | 387664 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.952 | 0.0475 | 125721 | 0 | 25 | 125746 | 0.0000994 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.87 | 284 | 456 | 0.623 | 0.0000305 | 5862 |
Missense in Polyphen | 125 | 272.19 | 0.45924 | 3118 | ||
Synonymous | -0.572 | 224 | 213 | 1.05 | 0.0000165 | 1949 |
Loss of Function | 4.39 | 5 | 31.6 | 0.158 | 0.00000152 | 396 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000580 | 0.0000580 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00105 | 0.00103 |
Finnish | 0.000139 | 0.0000924 |
European (Non-Finnish) | 0.0000193 | 0.0000176 |
Middle Eastern | 0.00105 | 0.00103 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has deubiquitinating activity towards 'Lys-11'-linked polyubiquitin chains. {ECO:0000269|PubMed:20622874, ECO:0000269|PubMed:23827681}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination
(Consensus)
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- loftool
- 0.0796
- rvis_EVS
- -1.15
- rvis_percentile_EVS
- 6.23
Haploinsufficiency Scores
- pHI
- 0.242
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.606
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.102
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Otud7a
- Phenotype
- growth/size/body region phenotype; craniofacial phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype;
Gene ontology
- Biological process
- protein deubiquitination;protein K11-linked deubiquitination;negative regulation of I-kappaB kinase/NF-kappaB signaling;protein K63-linked deubiquitination;protein K48-linked deubiquitination;protein deubiquitination involved in ubiquitin-dependent protein catabolic process
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- DNA binding;thiol-dependent ubiquitin-specific protease activity;zinc ion binding;thiol-dependent ubiquitinyl hydrolase activity;K63-linked polyubiquitin modification-dependent protein binding