KCNA10

potassium voltage-gated channel subfamily A member 10, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 1:110517217-110519175

Links

ENSG00000143105 ∙ NCBI:3744 ∙ OMIM:602420 ∙ HGNC:6219 ∙ Uniprot:Q16322 ∙ 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 KCNA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNA10 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					2	2
missense			29		3	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	5

Variants in KCNA10

This is a list of pathogenic ClinVar variants found in the KCNA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110517349-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-110517481-A-G		not specified	Uncertain significance (Aug 21, 2023)
1-110517490-C-A		not specified	Uncertain significance (Oct 12, 2022)
1-110517500-T-C		not specified	Uncertain significance (Sep 29, 2023)
1-110517527-T-C		not specified	Uncertain significance (Dec 20, 2021)
1-110517538-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-110517638-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-110517670-C-T			Benign (Aug 03, 2017)
1-110517699-G-T			Benign (Aug 08, 2017)
1-110517728-G-A		not specified	Uncertain significance (Nov 09, 2023)
1-110517826-G-A		not specified	Uncertain significance (Aug 14, 2023)
1-110517923-G-A		not specified	Uncertain significance (Mar 19, 2024)
1-110517944-A-G		not specified	Uncertain significance (Jun 13, 2024)
1-110517950-C-A		not specified	Uncertain significance (Sep 25, 2023)
1-110518004-G-C		not specified	Uncertain significance (Dec 15, 2023)
1-110518009-G-A		not specified	Uncertain significance (Mar 26, 2024)
1-110518027-T-C			Benign (Dec 28, 2017)
1-110518031-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-110518045-T-C		not specified	Uncertain significance (May 20, 2024)
1-110518064-G-A		not specified	Uncertain significance (Nov 30, 2021)
1-110518068-C-A		not specified	Uncertain significance (Oct 30, 2023)
1-110518093-A-C		not specified	Uncertain significance (Jun 09, 2022)
1-110518106-T-C		Congenital long QT syndrome	Uncertain significance (-)
1-110518114-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-110518122-C-T			Benign (Dec 28, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNA10	protein_coding	protein_coding	ENST00000369771	1	1959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000838	0.800	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.822	327	288	1.14	0.0000169	3387
Missense in Polyphen		142	133.05	1.0673		1555
Synonymous	-0.649	119	110	1.08	0.00000602	1032
Loss of Function	1.09	6	9.66	0.621	4.17e-7	131

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates 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. The channel activity is up-regulated by cAMP. {ECO:0000269|PubMed:10836990}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.168
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.54

Haploinsufficiency Scores

• pHI: 0.192
• hipred: Y
• hipred_score: 0.582
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.212

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcna10
• Phenotype: hearing/vestibular/ear phenotype

Gene ontology

• Biological process: potassium ion transport;regulation of ion transmembrane transport;protein homooligomerization;potassium ion transmembrane transport;potassium ion export across plasma membrane
• Cellular component: plasma membrane;voltage-gated potassium channel complex;integral component of membrane
• Molecular function: intracellular cyclic nucleotide activated cation channel activity;voltage-gated potassium channel activity;delayed rectifier potassium channel activity;outward rectifier potassium channel activity