GeneBe

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

  • complex neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCNA6 gene.

  • Inborn_genetic_diseases (42 variants)
  • not_provided (24 variants)
  • Pes_planus (1 variants)
  • Pyloric_stenosis (1 variants)
  • Moderate_global_developmental_delay (1 variants)
  • Epicanthus (1 variants)
  • Esophageal_atresia (1 variants)
  • Hypermetropia (1 variants)
  • Focal-onset_seizure (1 variants)
  • Cerebellar_ataxia (1 variants)
  • Inversion_of_nipple (1 variants)
  • Generalized-onset_seizure (1 variants)
  • Short_philtrum (1 variants)
  • Atypical_behavior (1 variants)
  • Macrocephaly (1 variants)

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. These statistics are base on transcript: NM_000002235.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
1
clinvar
61
clinvar
2
clinvar
 64
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 1 62 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KCNA6protein_codingprotein_codingENST00000433855 141936
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.4970.502125741071257480.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.051803380.5330.00002063423
Missense in Polyphen63178.180.353581818
Synonymous0.3221471520.9670.000009781151
Loss of Function2.84314.80.2038.55e-7135

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005780.0000578
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00004460.0000439
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.136

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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