KCNH4

potassium voltage-gated channel subfamily H member 4, the group of PAS domain containing|Potassium voltage-gated channels

Basic information

Region (hg38): 17:42156891-42181142

Links

ENSG00000089558 ∙ NCBI:23415 ∙ OMIM:604528 ∙ HGNC:6253 ∙ Uniprot:Q9UQ05 ∙ 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 KCNH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNH4 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	2
missense			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	49	2	1

Variants in KCNH4

This is a list of pathogenic ClinVar variants found in the KCNH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42160044-T-C		not specified	Uncertain significance (May 31, 2023)
17-42160050-G-A		not specified	Uncertain significance (Mar 28, 2023)
17-42160141-C-G		not specified	Uncertain significance (Oct 06, 2021)
17-42160149-T-C		not specified	Uncertain significance (Dec 13, 2023)
17-42160171-T-C		not specified	Uncertain significance (Dec 21, 2023)
17-42160172-C-G		not specified	Uncertain significance (Nov 26, 2024)
17-42160219-G-C		not specified	Uncertain significance (Jun 30, 2024)
17-42160331-G-A			Benign (Nov 14, 2018)
17-42160381-T-C		not specified	Uncertain significance (Mar 21, 2023)
17-42160390-G-A		not specified	Uncertain significance (Sep 23, 2023)
17-42160419-T-A		not specified	Uncertain significance (Jan 16, 2024)
17-42160428-C-T		not specified	Uncertain significance (May 02, 2024)
17-42162262-G-A		not specified	Uncertain significance (Mar 26, 2024)
17-42163248-C-T		not specified	Uncertain significance (Mar 31, 2023)
17-42163254-C-T		not specified	Uncertain significance (May 23, 2024)
17-42163634-T-C		not specified	Uncertain significance (Jan 08, 2024)
17-42163639-A-C		not specified	Uncertain significance (Jul 16, 2024)
17-42163642-G-A		not specified	Uncertain significance (Nov 13, 2023)
17-42163664-G-A		not specified	Uncertain significance (Jun 23, 2021)
17-42163688-G-C		not specified	Uncertain significance (Oct 10, 2023)
17-42163691-G-C		not specified	Uncertain significance (Oct 27, 2022)
17-42163729-G-C		not specified	Uncertain significance (May 17, 2023)
17-42163819-C-T		not specified	Uncertain significance (Oct 17, 2024)
17-42163829-C-T		not specified	Uncertain significance (Aug 14, 2023)
17-42163898-C-T		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNH4	protein_coding	protein_coding	ENST00000264661	16	24388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000160	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	435	645	0.674	0.0000423	6482
Missense in Polyphen		86	190	0.45263		2081
Synonymous	0.565	268	280	0.957	0.0000186	2239
Loss of Function	5.48	4	42.6	0.0940	0.00000229	450

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000972	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000709	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Pore-forming (alpha) subunit of voltage-gated potassium channel. Elicits an outward current, but shows no inactivation. Channel properties may be modulated by cAMP and subunit assembly.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.223

Intolerance Scores

• loftool: 0.00241
• rvis_EVS: -1.68
• rvis_percentile_EVS: 2.66

Haploinsufficiency Scores

• pHI: 0.370
• hipred: Y
• hipred_score: 0.774
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnh4
• Phenotype: immune system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: kcnh4a
• Affected structure: circadian sleep/wake cycle, sleep
• Phenotype tag: abnormal
• Phenotype quality: decreased duration

Gene ontology

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