KCNA6

potassium voltage-gated channel subfamily A member 6, the group of Potassium voltage-gated channels|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 12:4809334-4813318

Links

ENSG00000151079 ∙ NCBI:3742 ∙ OMIM:176257 ∙ HGNC:6225 ∙ Uniprot:P17658 ∙ 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 KCNA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNA6 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		1	15	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	15	1	0

Variants in KCNA6

This is a list of pathogenic ClinVar variants found in the KCNA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-4810060-C-T		Inborn genetic diseases	Uncertain significance (Dec 17, 2021)
12-4810087-C-T		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
12-4810117-G-C		Inborn genetic diseases	Uncertain significance (May 18, 2023)
12-4810193-G-A		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
12-4810274-A-G		Esophageal atresia;Pyloric stenosis	Uncertain significance (May 22, 2019)
12-4810325-C-T		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)
12-4810406-G-T		Inborn genetic diseases	Uncertain significance (Mar 11, 2024)
12-4810489-C-T		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
12-4810684-T-G		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
12-4810685-C-T		Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
12-4810731-T-G		Inborn genetic diseases	Uncertain significance (May 20, 2024)
12-4810768-A-G			Uncertain significance (Nov 06, 2023)
12-4810777-G-A		Inborn genetic diseases	Uncertain significance (Apr 09, 2024)
12-4810822-G-C			Uncertain significance (Jan 17, 2022)
12-4810883-G-C			Uncertain significance (Dec 13, 2023)
12-4810889-C-T			Uncertain significance (Nov 18, 2023)
12-4811167-C-G			Uncertain significance (Jun 20, 2022)
12-4811302-A-G			Uncertain significance (Dec 09, 2023)
12-4811333-T-C		Inborn genetic diseases	Uncertain significance (Jun 27, 2022)
12-4811351-T-C			Uncertain significance (Dec 18, 2023)
12-4811408-T-A		11 conditions	Likely pathogenic (Jan 31, 2023)
12-4811413-G-C			Uncertain significance (Mar 28, 2023)
12-4811461-C-G			Uncertain significance (Dec 09, 2023)
12-4811510-G-A		Inborn genetic diseases	Likely benign (Sep 14, 2021)
12-4811542-T-C		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNA6	protein_coding	protein_coding	ENST00000433855	1	41936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.497	0.502	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.05	180	338	0.533	0.0000206	3423
Missense in Polyphen		63	178.18	0.35358		1818
Synonymous	0.322	147	152	0.967	0.00000978	1151
Loss of Function	2.84	3	14.8	0.203	8.55e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes. Forms tetrameric potassium-selective channels through which potassium ions pass in accordance with their electrochemical gradient (PubMed:2347305, PubMed:14575698). The channel alternates between opened and closed conformations in response to the voltage difference across the membrane (PubMed:2347305, PubMed:14575698). Can form functional homotetrameric channels and heterotetrameric channels that contain variable proportions of KCNA1, KCNA2, KCNA4, KCNA6, and possibly other family members as well; channel properties depend on the type of alpha subunits that are part of the channel (By similarity). Channel properties are modulated by cytoplasmic beta subunits that regulate the subcellular location of the alpha subunits and promote rapid inactivation (By similarity). Homotetrameric channels display rapid activation and slow inactivation (PubMed:2347305). {ECO:0000250|UniProtKB:P17659, ECO:0000269|PubMed:14575698, ECO:0000269|PubMed:2347305}.
• Pathway: Post-translational protein modification;Metabolism of proteins;mucin core 1 and core 2 <i>O</i>-glycosylation;Neuronal System;O-Glycan biosynthesis;Voltage gated Potassium channels;Potassium Channels;O-linked glycosylation of mucins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.0657
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.765
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcna6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: potassium ion transport;regulation of ion transmembrane transport;protein homooligomerization;potassium ion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;voltage-gated potassium channel complex;integral component of membrane;potassium channel complex;axon terminus
• Molecular function: voltage-gated potassium channel activity;delayed rectifier potassium channel activity