KCTD4

potassium channel tetramerization domain containing 4, the group of KCTD family

Basic information

Region (hg38): 13:45192853-45201045

Links

ENSG00000180332 ∙ NCBI:386618 ∙ ∙ HGNC:23227 ∙ Uniprot:Q8WVF5 ∙ 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 KCTD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD4 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in KCTD4

This is a list of pathogenic ClinVar variants found in the KCTD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-45193822-A-G		not specified	Uncertain significance (Jan 24, 2023)
13-45193909-A-C		not specified	Uncertain significance (Jun 18, 2021)
13-45193990-A-G		not specified	Uncertain significance (Apr 13, 2022)
13-45194056-C-T		not specified	Uncertain significance (Sep 20, 2023)
13-45194057-G-A		not specified	Uncertain significance (Jan 22, 2024)
13-45194081-C-G		not specified	Uncertain significance (Aug 02, 2023)
13-45194119-T-A		not specified	Uncertain significance (Jan 04, 2022)
13-45194300-G-C		not specified	Uncertain significance (Jan 02, 2024)
13-45194359-G-A		not specified	Uncertain significance (Aug 26, 2022)
13-45194539-T-C		not specified	Uncertain significance (Jun 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD4	protein_coding	protein_coding	ENST00000405872	1	8188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00314	0.834	125611	0	117	125728	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.782	108	133	0.809	0.00000702	1708
Missense in Polyphen		37	46.895	0.789		569
Synonymous	-1.37	63	50.6	1.25	0.00000271	500
Loss of Function	1.16	5	8.67	0.577	6.13e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00595	0.00591
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000888	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000996	0.0000980
Other	0.000170	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.509
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.239
• hipred: N
• hipred_score: 0.325
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd4

Gene ontology

• Biological process: protein homooligomerization
• Molecular function: protein binding