KCTD12
Basic information
Region (hg38): 13:76880175-76886405
Previous symbols: [ "C13orf2" ]
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 KCTD12 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 | 12 | 12 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 12 | 0 | 2 |
Variants in KCTD12
This is a list of pathogenic ClinVar variants found in the KCTD12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
13-76885276-C-T | not specified | Uncertain significance (Feb 17, 2023) | ||
13-76885290-A-C | not specified | Uncertain significance (Apr 07, 2023) | ||
13-76885367-C-A | not specified | Uncertain significance (Dec 22, 2023) | ||
13-76885468-G-C | not specified | Uncertain significance (Jan 02, 2024) | ||
13-76885480-G-T | not specified | Uncertain significance (Oct 27, 2022) | ||
13-76885513-G-C | not specified | Uncertain significance (Oct 24, 2023) | ||
13-76885543-G-C | not specified | Uncertain significance (Jan 02, 2024) | ||
13-76885553-T-A | not specified | Uncertain significance (Dec 19, 2022) | ||
13-76885593-G-C | not specified | Uncertain significance (May 02, 2024) | ||
13-76885692-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
13-76885888-G-A | Benign (Jul 03, 2018) | |||
13-76885922-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
13-76885945-C-T | Benign (Jun 18, 2018) | |||
13-76885953-G-C | not specified | Uncertain significance (Apr 26, 2024) | ||
13-76885961-A-G | not specified | Uncertain significance (Jun 05, 2024) | ||
13-76885964-C-A | not specified | Uncertain significance (Apr 26, 2024) | ||
13-76885992-C-T | not specified | Uncertain significance (May 12, 2024) | ||
13-76886076-A-T | not specified | Uncertain significance (Dec 06, 2022) | ||
13-76886085-A-T | not specified | Uncertain significance (May 23, 2024) | ||
13-76886127-G-C | not specified | Uncertain significance (Jul 19, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KCTD12 | protein_coding | protein_coding | ENST00000377474 | 1 | 6229 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0617 | 0.876 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.762 | 145 | 173 | 0.837 | 0.00000794 | 2011 |
Missense in Polyphen | 28 | 57.176 | 0.48971 | 628 | ||
Synonymous | -2.54 | 112 | 82.6 | 1.36 | 0.00000403 | 703 |
Loss of Function | 1.57 | 3 | 7.69 | 0.390 | 3.29e-7 | 89 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Auxiliary subunit of GABA-B receptors that determine the pharmacology and kinetics of the receptor response. Increases agonist potency and markedly alter the G-protein signaling of the receptors by accelerating onset and promoting desensitization (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.129
Haploinsufficiency Scores
- pHI
- 0.776
- hipred
- N
- hipred_score
- 0.468
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.834
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kctd12
- 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
- kctd12.2
- Affected structure
- ventral habenular nucleus
- Phenotype tag
- abnormal
- Phenotype quality
- increased volume
Gene ontology
- Biological process
- protein homooligomerization
- Cellular component
- cell junction;presynaptic membrane;postsynaptic membrane
- Molecular function
- RNA binding;identical protein binding