KCTD6

potassium channel tetramerization domain containing 6, the group of KCTD family

Basic information

Region (hg38): 3:58492096-58502360

Links

ENSG00000168301 ∙ NCBI:200845 ∙ OMIM:618791 ∙ HGNC:22235 ∙ Uniprot:Q8NC69 ∙ 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 KCTD6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD6 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 KCTD6

This is a list of pathogenic ClinVar variants found in the KCTD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-58501010-C-T		not specified	Uncertain significance (Sep 27, 2022)
3-58501529-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-58501535-G-A		not specified	Uncertain significance (May 12, 2024)
3-58501537-A-C		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD6	protein_coding	protein_coding	ENST00000355076	2	10247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0169	0.897	125739	0	4	125743	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	61	129	0.473	0.00000722	1563
Missense in Polyphen		9	34.043	0.26437		389
Synonymous	0.757	41	47.6	0.861	0.00000256	463
Loss of Function	1.45	4	8.57	0.467	5.79e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate-specific adapter of a BCR (BTB-CUL3- RBX1) E3 ubiquitin-protein ligase complex mediating the ubiquitination and subsequent proteasomal degradation of target proteins. Promotes the ubiquitination of HDAC1; the function seems to depend on KCTD11:KCTD6 oligomerization. Can function as antagonist of the Hedgehog pathway by affecting the nuclear transfer of transcription factor GLI1; the function probably occurs via HDAC1 down-regulation, keeping GLI1 acetylated and inactive. Inhibits cell growth and tumorigenicity of medulloblastoma (MDB) (PubMed:21472142). Involved in regulating protein levels of ANK1 isoform Mu17 probably implicating CUL3- dependent proteasomal degradation (PubMed:22573887). {ECO:0000269|PubMed:21472142, ECO:0000269|PubMed:22573887}.
• Pathway: Transcriptional regulation by RUNX1;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;RNA Polymerase II Transcription;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;RUNX1 regulates estrogen receptor mediated transcription;ESR-mediated signaling;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• loftool: 0.300
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.365
• hipred: N
• hipred_score: 0.476
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd6

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;regulation of intracellular estrogen receptor signaling pathway;regulation of growth;post-translational protein modification;negative regulation of smoothened signaling pathway;protein homooligomerization
• Cellular component: cytosol;M band
• Molecular function: protein binding;ankyrin binding;identical protein binding;cullin family protein binding