KCNA3

potassium voltage-gated channel subfamily A member 3, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 1:110653560-110674940

Links

ENSG00000177272 ∙ NCBI:3738 ∙ OMIM:176263 ∙ HGNC:6221 ∙ Uniprot:P22001 ∙ 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 KCNA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNA3 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		13	30			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	13	30	0	2

Variants in KCNA3

This is a list of pathogenic ClinVar variants found in the KCNA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-110673155-G-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2022)
1-110673174-G-A		Inborn genetic diseases	Uncertain significance (Jul 14, 2021)
1-110673184-G-A			Benign (Feb 09, 2018)
1-110673199-C-G		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
1-110673200-A-G		Inborn genetic diseases	Uncertain significance (Jan 19, 2024)
1-110673206-C-G		Inborn genetic diseases	Uncertain significance (Feb 14, 2024)
1-110673236-C-T		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Nov 21, 2023)
1-110673378-C-T		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673380-G-T		KCNA3-associated disorder • KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673407-C-A		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Nov 21, 2023)
1-110673407-CC-AA		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673408-C-G		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Nov 21, 2023)
1-110673432-C-T		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673447-T-C		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673482-G-A		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673518-A-T		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673539-G-A		Inborn genetic diseases	Uncertain significance (Feb 03, 2022)
1-110673618-G-C		KCNA3-related disorder	Uncertain significance (Feb 26, 2024)
1-110673729-C-T		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673740-G-A		KCNA3-associated developmental and epileptic encephalopathy	Likely pathogenic (Feb 14, 2023)
1-110673744-G-C			Uncertain significance (Jul 05, 2022)
1-110673954-C-A		Inborn genetic diseases	Uncertain significance (Feb 23, 2023)
1-110673957-G-C		Inborn genetic diseases	Uncertain significance (Jul 06, 2022)
1-110673962-C-T		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
1-110673996-C-A		Inborn genetic diseases	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNA3	protein_coding	protein_coding	ENST00000369769	1	3346

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.894	0.106	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.02	194	354	0.549	0.0000215	3719
Missense in Polyphen		43	158.43	0.27141		1635
Synonymous	1.18	145	164	0.883	0.0000110	1230
Loss of Function	3.25	2	16.1	0.124	9.64e-7	154

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 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: Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Neuronal System;BDNF;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.228

Intolerance Scores

• loftool: 0.235
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.287
• ghis: 0.446

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.676

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcna3
• Phenotype: growth/size/body region phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; normal 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;axon;calyx of Held;membrane raft;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
• Molecular function: voltage-gated ion channel activity;voltage-gated potassium channel activity;delayed rectifier potassium channel activity;protein binding;outward rectifier potassium channel activity