KCTD10

potassium channel tetramerization domain containing 10, the group of KCTD family|BTB domain containing

Basic information

Region (hg38): 12:109448655-109477359

Links

ENSG00000110906

∙ NCBI:83892 ∙ OMIM:613421 ∙ HGNC:23236 ∙ Uniprot:Q9H3F6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

multiple congenital anomalies/dysmorphic syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD10 gene.

not_specified (20 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031954.5. 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						0
missense			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD10	protein_coding	protein_coding	ENST00000228495	7	28889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.863	0.137	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	110	205	0.537	0.0000135	2034
Missense in Polyphen		22	68.958	0.31904		795
Synonymous	-0.0663	88	87.2	1.01	0.00000598	619
Loss of Function	3.15	2	15.3	0.131	7.10e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex. The BCR(BACURD3) E3 ubiquitin ligase complex mediates the ubiquitination of target proteins, leading to their degradation by the proteasome (By similarity). {ECO:0000250|UniProtKB:Q8WZ19}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

loftool: 0.333
rvis_EVS: -0.16
rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

pHI: 0.313
hipred: Y
hipred_score: 0.752
ghis: 0.591

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.882

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Kctd10
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: kctd10
Affected structure: endocardium
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;protein homooligomerization
Cellular component: nucleoplasm;cytosol;Cul3-RING ubiquitin ligase complex
Molecular function: ubiquitin-protein transferase activity;Notch binding;protein binding