KCTD10

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

Basic information

Region (hg38): 12:109448654-109477359

Links

ENSG00000110906 ∙ NCBI:83892 ∙ OMIM:613421 ∙ HGNC:23236 ∙ Uniprot:Q9H3F6 ∙ 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 KCTD10 gene.

• Inborn genetic diseases (3 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.

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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in KCTD10

This is a list of pathogenic ClinVar variants found in the KCTD10 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-109451673-G-C		not specified	Uncertain significance (Feb 07, 2023)
12-109451678-C-T		not specified	Uncertain significance (Oct 31, 2023)
12-109451695-C-T		not specified	Uncertain significance (Jan 23, 2023)
12-109451744-G-A		not specified	Uncertain significance (Jan 24, 2024)
12-109456252-T-A		not specified	Uncertain significance (Mar 04, 2024)
12-109458068-G-T		not specified	Uncertain significance (Dec 06, 2023)
12-109460715-C-T		not specified	Uncertain significance (Feb 23, 2023)
12-109460721-C-A		not specified	Uncertain significance (May 08, 2023)
12-109469685-G-A		not specified	Uncertain significance (Jan 03, 2024)

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