KCTD13

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

Basic information

Region (hg38): 16:29905012-29926236

Links

ENSG00000174943

∙ NCBI:253980 ∙ OMIM:608947 ∙ HGNC:22234 ∙ Uniprot:Q8WZ19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (37 variants)
KCTD13-related_disorder (4 variants)

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. These statistics are base on transcript: NM_000178863.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			36 clinvar			36
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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