KCTD13

potassium channel tetramerization domain containing 13, the group of KCTD family

Basic information

Region (hg38): 16:29905012-29926236

Links

ENSG00000174943NCBI:253980OMIM:608947HGNC:22234Uniprot:Q8WZ19AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD13 gene.

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
clinvar
2
missense
13
clinvar
13
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)3130446
16-29905803-G-A not specified Uncertain significance (Jan 09, 2024)3130447
16-29905822-C-G not specified Uncertain significance (Jan 20, 2023)2476993
16-29905859-C-T not specified Uncertain significance (Nov 21, 2022)2328548
16-29905891-C-A not specified Uncertain significance (Aug 12, 2021)2243312
16-29906951-C-T not specified Uncertain significance (Feb 09, 2022)2264501
16-29907038-G-A not specified Uncertain significance (Mar 25, 2024)3287812
16-29907047-G-A not specified Uncertain significance (Jul 05, 2023)2602042
16-29907071-AG-A not specified Uncertain significance (May 04, 2022)1684831
16-29911050-G-A KCTD13-related disorder Likely benign (Apr 03, 2019)3057318
16-29911140-C-G not specified Uncertain significance (Dec 30, 2023)3113609
16-29923211-C-A not specified Uncertain significance (Nov 10, 2022)2325829
16-29923218-A-C not specified Uncertain significance (Jun 24, 2022)2296378
16-29923226-C-T KCTD13-related disorder Likely benign (Apr 08, 2019)3057985
16-29923272-G-A not specified Uncertain significance (May 27, 2022)2292958
16-29923311-T-C not specified Uncertain significance (Jul 05, 2023)2590360
16-29923315-G-A not specified Uncertain significance (Mar 07, 2023)2464409
16-29923333-G-A not specified Uncertain significance (Jun 18, 2024)3287811
16-29923336-C-T not specified Uncertain significance (Feb 28, 2023)2462423
16-29925829-T-G not specified Uncertain significance (Jan 24, 2024)2409861
16-29925839-C-T not specified Uncertain significance (May 15, 2024)3287814
16-29925959-C-G not specified Uncertain significance (Jun 11, 2021)2232595
16-29925961-C-G not specified Uncertain significance (Feb 23, 2023)2455629
16-29925970-A-C KCTD13-related disorder Uncertain significance (Jun 27, 2024)3354065
16-29925985-C-T not specified Uncertain significance (Feb 15, 2023)2462857

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KCTD13protein_codingprotein_codingENST00000568000 622024
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0009150.9461257310141257450.0000557
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.921382180.6340.00001412086
Missense in Polyphen3280.1960.39902740
Synonymous0.5169096.40.9330.00000586713
Loss of Function1.71713.90.5056.75e-7155

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002470.000243
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00006210.0000615
Middle Eastern0.000.00
South Asian0.00006550.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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