KCNH6

potassium voltage-gated channel subfamily H member 6, the group of Potassium voltage-gated channels|PAS domain containing

Basic information

Region (hg38): 17:63523333-63548977

Links

ENSG00000173826 ∙ NCBI:81033 ∙ OMIM:608168 ∙ HGNC:18862 ∙ Uniprot:Q9H252 ∙ 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 KCNH6 gene.

• Inborn genetic diseases (51 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNH6 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	1	3
missense			53			53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	2	1

Variants in KCNH6

This is a list of pathogenic ClinVar variants found in the KCNH6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63523477-T-C		not specified	Uncertain significance (Feb 03, 2023)
17-63524142-G-A		not specified	Uncertain significance (Mar 06, 2023)
17-63524152-G-T			Benign (Nov 10, 2017)
17-63524160-A-G		not specified	Uncertain significance (Feb 27, 2024)
17-63524177-T-C		not specified	Uncertain significance (Jan 09, 2024)
17-63524179-C-T			Likely benign (Jul 01, 2022)
17-63524229-G-A		not specified	Uncertain significance (May 25, 2022)
17-63524297-G-A		not specified	Likely benign (Dec 09, 2023)
17-63530126-G-A		not specified	Uncertain significance (Feb 15, 2023)
17-63530134-C-G		not specified	Uncertain significance (Jul 07, 2022)
17-63530137-G-C		not specified	Uncertain significance (Oct 31, 2023)
17-63530174-G-T		not specified	Uncertain significance (Jun 02, 2023)
17-63530241-T-A		not specified	Uncertain significance (Jan 16, 2024)
17-63530394-G-A			Uncertain significance (Jul 18, 2020)
17-63533902-C-T		not specified	Uncertain significance (Aug 29, 2022)
17-63533915-G-A			Likely benign (Feb 01, 2023)
17-63533982-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-63534069-G-A		not specified	Uncertain significance (Dec 19, 2023)
17-63534092-C-G		not specified	Uncertain significance (Jun 06, 2023)
17-63534097-C-G		not specified	Uncertain significance (Jun 06, 2023)
17-63534129-G-A		not specified	Uncertain significance (Mar 13, 2023)
17-63534196-A-G		not specified	Uncertain significance (May 23, 2023)
17-63534217-G-A		not specified	Uncertain significance (Mar 11, 2024)
17-63534225-G-A		not specified	Uncertain significance (Nov 01, 2022)
17-63534243-T-C		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNH6	protein_coding	protein_coding	ENST00000583023	14	25644

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.12e-31	0.0000115	125395	1	352	125748	0.00140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.205	632	618	1.02	0.0000395	6442
Missense in Polyphen		204	200.82	1.0158		1997
Synonymous	0.00222	272	272	1.00	0.0000186	2065
Loss of Function	-0.529	44	40.4	1.09	0.00000207	424

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00300	0.00299
Ashkenazi Jewish	0.00182	0.00179
East Asian	0.00337	0.00332
Finnish	0.000419	0.000416
European (Non-Finnish)	0.00101	0.000976
Middle Eastern	0.00337	0.00332
South Asian	0.00233	0.00229
Other	0.00148	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits a slowly activating, rectifying current (By similarity). Channel properties may be modulated by cAMP and subunit assembly. {ECO:0000250}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.0284
• rvis_EVS: -0.61
• rvis_percentile_EVS: 17.51

Haploinsufficiency Scores

• pHI: 0.300
• hipred: N
• hipred_score: 0.477
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnh6

Zebrafish Information Network

• Gene name: kcnh6a
• Affected structure: parachordal vessel
• Phenotype tag: abnormal
• Phenotype quality: present

Gene ontology

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