KCNG4

potassium voltage-gated channel modifier subfamily G member 4, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 16:84218657-84240012

Links

ENSG00000168418 ∙ NCBI:93107 ∙ OMIM:607603 ∙ HGNC:19697 ∙ Uniprot:Q8TDN1 ∙ 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 KCNG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNG4 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					3	3
missense			46	2	2	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	2	5

Variants in KCNG4

This is a list of pathogenic ClinVar variants found in the KCNG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84222306-C-T		not specified	Uncertain significance (Sep 14, 2022)
16-84222315-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-84222326-G-C		not specified	Uncertain significance (Apr 12, 2022)
16-84222328-T-C			Benign (Dec 28, 2017)
16-84222372-C-G		not specified	Uncertain significance (Jan 04, 2022)
16-84222372-C-T		not specified	Uncertain significance (Apr 20, 2024)
16-84222390-C-T		not specified	Uncertain significance (May 13, 2024)
16-84222411-T-C		not specified	Uncertain significance (May 22, 2023)
16-84222420-T-C		not specified	Uncertain significance (May 08, 2024)
16-84222425-G-A		not specified	Uncertain significance (Nov 22, 2021)
16-84222477-C-A		not specified	Uncertain significance (Jul 14, 2021)
16-84222498-G-A		not specified	Uncertain significance (Jul 12, 2022)
16-84222522-C-T			Benign (Dec 31, 2019)
16-84222524-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-84222558-C-G		not specified	Uncertain significance (Apr 25, 2023)
16-84222576-C-T		not specified	Uncertain significance (Jul 08, 2022)
16-84222619-G-A			Benign (Dec 31, 2019)
16-84222639-C-T		not specified	Uncertain significance (May 04, 2023)
16-84222671-C-T		not specified	Uncertain significance (Feb 16, 2023)
16-84222687-C-T		not specified	Uncertain significance (Oct 10, 2023)
16-84222716-G-A		not specified	Uncertain significance (Apr 08, 2024)
16-84222729-G-T		not specified	Uncertain significance (Dec 17, 2021)
16-84222795-A-G		not specified	Uncertain significance (Jan 11, 2023)
16-84222830-G-T		not specified	Uncertain significance (Dec 16, 2023)
16-84222844-C-T			Benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNG4	protein_coding	protein_coding	ENST00000308251	2	17534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.21e-16	0.000850	125697	0	47	125744	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.66	434	347	1.25	0.0000235	3358
Missense in Polyphen		215	171.97	1.2502		1606
Synonymous	-2.60	204	162	1.26	0.0000120	1092
Loss of Function	-1.49	20	14.0	1.43	6.86e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000445	0.000435
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000184	0.000176
Middle Eastern	0.000445	0.000435
South Asian	0.000264	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potassium channel subunit that does not form functional channels by itself. Can form functional heterotetrameric channels with KCNB1; modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1 (PubMed:19074135). {ECO:0000269|PubMed:19074135}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.147
• rvis_EVS: 1.43
• rvis_percentile_EVS: 95

Haploinsufficiency Scores

• pHI: 0.0772
• hipred: N
• hipred_score: 0.251
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.218

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Kcng4
• 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: kcng4b
• Affected structure: neuroepithelial cell
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

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