KCNK13

potassium two pore domain channel subfamily K member 13, the group of Potassium two pore domain channel subfamily K

Basic information

Region (hg38): 14:90061993-90185853

Links

ENSG00000152315 ∙ NCBI:56659 ∙ OMIM:607367 ∙ HGNC:6275 ∙ Uniprot:Q9HB14 ∙ 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 KCNK13 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNK13 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				1		1
missense			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	3	0

Variants in KCNK13

This is a list of pathogenic ClinVar variants found in the KCNK13 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-90062209-G-A		not specified	Uncertain significance (Mar 14, 2024)
14-90062220-T-G			Likely benign (Aug 01, 2023)
14-90062225-G-A		not specified	Uncertain significance (Jul 12, 2022)
14-90062364-G-C		not specified	Uncertain significance (Jan 03, 2022)
14-90062392-G-C		not specified	Likely benign (Apr 07, 2023)
14-90062419-C-T		not specified	Uncertain significance (Apr 24, 2023)
14-90062463-C-G		not specified	Uncertain significance (Jun 30, 2023)
14-90062496-C-A		not specified	Uncertain significance (Aug 10, 2021)
14-90062510-A-C		not specified	Uncertain significance (Dec 20, 2023)
14-90184137-G-A		not specified	Uncertain significance (Feb 28, 2023)
14-90184168-G-T		not specified	Uncertain significance (Feb 02, 2024)
14-90184170-C-T			Likely benign (Aug 01, 2023)
14-90184242-A-G		not specified	Uncertain significance (Jul 06, 2021)
14-90184405-G-A		not specified	Uncertain significance (Feb 10, 2022)
14-90184525-A-G		not specified	Uncertain significance (Jan 19, 2024)
14-90184572-C-T		not specified	Uncertain significance (Jul 09, 2021)
14-90184675-C-T		not specified	Uncertain significance (Mar 01, 2023)
14-90184705-G-A		not specified	Uncertain significance (Mar 22, 2023)
14-90184776-G-C		not specified	Uncertain significance (Jul 15, 2021)
14-90184786-C-T		not specified	Uncertain significance (Jun 22, 2023)
14-90184798-G-A		not specified	Uncertain significance (May 03, 2023)
14-90184836-G-T		not specified	Uncertain significance (May 08, 2023)
14-90184842-A-G		not specified	Uncertain significance (Jun 28, 2023)
14-90184920-G-T		not specified	Likely benign (Jan 29, 2024)
14-90184923-C-T		not specified	Uncertain significance (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNK13	protein_coding	protein_coding	ENST00000282146	2	124093

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0526	0.929	125736	0	9	125745	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.743	197	229	0.862	0.0000141	2642
Missense in Polyphen		48	70.51	0.68075		897
Synonymous	0.345	90	94.3	0.955	0.00000578	829
Loss of Function	2.05	4	11.5	0.347	6.84e-7	125

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potassium channel displaying weak inward rectification in symmetrical K(+) solution. {ECO:0000250}.
• Pathway: Neuronal System;Phase 4 - resting membrane potential;Cardiac conduction;Muscle contraction;Tandem pore domain halothane-inhibited K+ channel (THIK);Tandem pore domain potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.334
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.55

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.507
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnk13
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: stabilization of membrane potential;regulation of ion transmembrane transport;potassium ion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: voltage-gated ion channel activity;potassium channel activity;potassium ion leak channel activity