KCTD13
Basic information
Region (hg38): 16:29905012-29926236
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD13 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 | 2 | |||||
missense | 13 | 13 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 14 | 3 | 0 |
Variants in KCTD13
This is a list of pathogenic ClinVar variants found in the KCTD13 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-29905796-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
16-29905803-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
16-29905822-C-G | not specified | Uncertain significance (Jan 20, 2023) | ||
16-29905859-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
16-29905891-C-A | not specified | Uncertain significance (Aug 12, 2021) | ||
16-29906951-C-T | not specified | Uncertain significance (Feb 09, 2022) | ||
16-29907038-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
16-29907047-G-A | not specified | Uncertain significance (Jul 05, 2023) | ||
16-29907071-AG-A | not specified | Uncertain significance (May 04, 2022) | ||
16-29911050-G-A | KCTD13-related disorder | Likely benign (Apr 03, 2019) | ||
16-29911140-C-G | not specified | Uncertain significance (Dec 30, 2023) | ||
16-29923211-C-A | not specified | Uncertain significance (Nov 10, 2022) | ||
16-29923218-A-C | not specified | Uncertain significance (Jun 24, 2022) | ||
16-29923226-C-T | KCTD13-related disorder | Likely benign (Apr 08, 2019) | ||
16-29923272-G-A | not specified | Uncertain significance (May 27, 2022) | ||
16-29923311-T-C | not specified | Uncertain significance (Jul 05, 2023) | ||
16-29923315-G-A | not specified | Uncertain significance (Mar 07, 2023) | ||
16-29923333-G-A | not specified | Uncertain significance (Jun 18, 2024) | ||
16-29923336-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
16-29925829-T-G | not specified | Uncertain significance (Jan 24, 2024) | ||
16-29925839-C-T | not specified | Uncertain significance (May 15, 2024) | ||
16-29925959-C-G | not specified | Uncertain significance (Jun 11, 2021) | ||
16-29925961-C-G | not specified | Uncertain significance (Feb 23, 2023) | ||
16-29925970-A-C | KCTD13-related disorder | Uncertain significance (Jun 27, 2024) | ||
16-29925985-C-T | not specified | Uncertain significance (Feb 15, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KCTD13 | protein_coding | protein_coding | ENST00000568000 | 6 | 22024 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000915 | 0.946 | 125731 | 0 | 14 | 125745 | 0.0000557 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.92 | 138 | 218 | 0.634 | 0.0000141 | 2086 |
Missense in Polyphen | 32 | 80.196 | 0.39902 | 740 | ||
Synonymous | 0.516 | 90 | 96.4 | 0.933 | 0.00000586 | 713 |
Loss of Function | 1.71 | 7 | 13.9 | 0.505 | 6.75e-7 | 155 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000247 | 0.000243 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000621 | 0.0000615 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000655 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for synaptic transmission (PubMed:19782033). The BCR(KCTD13) E3 ubiquitin ligase complex mediates the ubiquitination of RHOA, leading to its degradation by the proteasome (PubMed:19782033) Degradation of RHOA regulates the actin cytoskeleton and promotes synaptic transmission (By similarity). {ECO:0000250|UniProtKB:Q8BGV7, ECO:0000269|PubMed:19782033}.;
- Disease
- DISEASE: Note=The gene represented in this entry may act as a disease modifier for autism and schizophrenia associated with recurrent deletions and duplications of chromosome 16p11.2 region (PubMed:22596160, PubMed:25695269). {ECO:0000269|PubMed:22596160, ECO:0000269|PubMed:25695269}.;
Recessive Scores
- pRec
- 0.0884
Intolerance Scores
- loftool
- 0.253
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.383
- hipred
- Y
- hipred_score
- 0.840
- ghis
- 0.607
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.925
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kctd13
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);
Zebrafish Information Network
- Gene name
- kctd13
- Affected structure
- white matter
- Phenotype tag
- abnormal
- Phenotype quality
- spatial pattern
Gene ontology
- Biological process
- DNA replication;cell migration;protein ubiquitination;negative regulation of Rho protein signal transduction;stress fiber assembly;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of DNA replication;positive regulation of synaptic transmission;protein homooligomerization;neural precursor cell proliferation
- Cellular component
- nucleus;nuclear body;Cul3-RING ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;GTP-Rho binding;protein domain specific binding;identical protein binding