KCNK5

potassium two pore domain channel subfamily K member 5, the group of Potassium two pore domain channel subfamily K

Basic information

Region (hg38): 6:39188971-39229475

Links

ENSG00000164626 ∙ NCBI:8645 ∙ OMIM:603493 ∙ HGNC:6280 ∙ Uniprot:O95279 ∙ 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 KCNK5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNK5 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			28	2	2	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	28	4	2

Variants in KCNK5

This is a list of pathogenic ClinVar variants found in the KCNK5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-39190997-G-T			Benign (Oct 29, 2020)
6-39191065-T-C		not specified	Uncertain significance (Sep 16, 2021)
6-39191171-C-T			Benign (Nov 02, 2017)
6-39191183-C-T		not specified	Uncertain significance (Mar 02, 2023)
6-39191205-C-T			Likely benign (Apr 10, 2018)
6-39191217-G-C		not specified	Uncertain significance (Sep 14, 2023)
6-39191225-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-39191249-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-39191264-C-G		not specified	Uncertain significance (Jan 30, 2024)
6-39191288-C-T		not specified	Uncertain significance (Oct 02, 2023)
6-39191296-T-A		KCNK5-related disorder	Likely benign (Mar 18, 2022)
6-39191308-G-A		not specified	Uncertain significance (Dec 03, 2021)
6-39191336-C-T		not specified	Uncertain significance (Oct 12, 2021)
6-39191339-G-A		not specified	Uncertain significance (Feb 02, 2022)
6-39191396-C-T		KCNK5-related disorder	Likely benign (May 09, 2022)
6-39191441-C-G		not specified	Uncertain significance (Dec 14, 2023)
6-39191442-G-A			Likely benign (Feb 01, 2024)
6-39191461-T-C		not specified	Uncertain significance (Nov 07, 2022)
6-39191528-C-T		not specified	Uncertain significance (Jan 06, 2023)
6-39191570-G-C		not specified	Uncertain significance (Jun 09, 2022)
6-39191611-C-T		not specified	Uncertain significance (Aug 09, 2021)
6-39191720-G-A		not specified	Uncertain significance (Jul 08, 2022)
6-39194262-C-T		not specified	Uncertain significance (Oct 13, 2023)
6-39194301-C-T		not specified	Uncertain significance (Apr 12, 2022)
6-39194321-G-A		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNK5	protein_coding	protein_coding	ENST00000359534	5	40478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.325	0.674	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.97	203	299	0.680	0.0000185	3238
Missense in Polyphen		63	120.09	0.52462		1294
Synonymous	-0.284	138	134	1.03	0.00000917	1027
Loss of Function	2.95	4	17.2	0.232	8.30e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: pH-dependent, voltage insensitive, outwardly rectifying potassium channel. Outward rectification is lost at high external K(+) concentrations.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Taste transduction - Homo sapiens (human);Phase 4 - resting membrane potential;Cardiac conduction;Muscle contraction (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.160
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.506
• hipred: Y
• hipred_score: 0.728
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.587

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnk5
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region 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); renal/urinary system phenotype; respiratory system phenotype

Zebrafish Information Network

• Gene name: kcnk5b
• Affected structure: lepidotrichium segment
• Phenotype tag: abnormal
• Phenotype quality: increased variability of size

Gene ontology

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