KCNC4

potassium voltage-gated channel subfamily C member 4, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 1:110210313-110283100

Previous symbols: [ "C1orf30" ]

Links

ENSG00000116396 ∙ NCBI:3749 ∙ OMIM:176265 ∙ HGNC:6236 ∙ Uniprot:Q03721 ∙ 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 KCNC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNC4 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				3		3
missense			39	4		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	7	0

Variants in KCNC4

This is a list of pathogenic ClinVar variants found in the KCNC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110211633-C-T		not specified	Uncertain significance (Mar 11, 2024)
1-110211704-G-T		not specified	Uncertain significance (Dec 28, 2023)
1-110211725-A-T		not specified	Likely benign (Apr 07, 2023)
1-110211741-T-C		not specified	Likely benign (Apr 07, 2023)
1-110211801-G-A		not specified	Uncertain significance (May 18, 2022)
1-110211995-G-C		not specified	Uncertain significance (Dec 16, 2023)
1-110212004-A-G		not specified	Likely benign (Apr 07, 2023)
1-110212006-C-G		not specified	Uncertain significance (Apr 07, 2023)
1-110212008-G-C		not specified	Uncertain significance (Apr 07, 2023)
1-110212019-A-G		not specified	Likely benign (Aug 12, 2021)
1-110212028-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-110212046-G-A		not specified	Uncertain significance (Apr 15, 2024)
1-110212066-G-C			Likely benign (Mar 01, 2024)
1-110212076-G-C		not specified	Uncertain significance (Jan 11, 2023)
1-110212085-G-C		not specified	Uncertain significance (Mar 31, 2022)
1-110212097-G-T		not specified	Uncertain significance (May 23, 2024)
1-110212098-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-110212104-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-110212142-C-T		not specified	Uncertain significance (May 20, 2024)
1-110223045-G-A		not specified	Uncertain significance (Nov 30, 2022)
1-110223052-A-G		not specified	Uncertain significance (Oct 12, 2022)
1-110223071-C-T			Likely benign (Mar 29, 2018)
1-110223081-A-G		not specified	Uncertain significance (Jan 16, 2024)
1-110223090-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-110223298-C-G		not specified	Uncertain significance (Feb 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNC4	protein_coding	protein_coding	ENST00000369787	4	71758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00445	0.989	125729	0	16	125745	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	302	421	0.717	0.0000269	4082
Missense in Polyphen		86	186.95	0.46001		1906
Synonymous	-0.365	193	187	1.03	0.0000121	1388
Loss of Function	2.40	7	18.0	0.390	9.20e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000990	0.0000967
Middle Eastern	0.0000551	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein mediates the voltage-dependent potassium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.0533
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.79

Haploinsufficiency Scores

• pHI: 0.590
• hipred: N
• hipred_score: 0.417
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.326

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnc4

Gene ontology

• Biological process: potassium ion transport;chemical synaptic transmission;regulation of ion transmembrane transport;regulation of neurotransmitter secretion;protein homooligomerization;potassium ion transmembrane transport
• Cellular component: plasma membrane;voltage-gated potassium channel complex;integral component of membrane;axon;neuromuscular junction;dendrite membrane;neuronal cell body membrane;neuronal cell body;axon terminus
• Molecular function: voltage-gated potassium channel activity;delayed rectifier potassium channel activity;potassium channel activity