KCNF1

potassium voltage-gated channel modifier subfamily F member 1, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 2:10911934-10914225

Previous symbols: [ "KCNF" ]

Links

ENSG00000162975 ∙ NCBI:3754 ∙ OMIM:603787 ∙ HGNC:6246 ∙ Uniprot:Q9H3M0 ∙ 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 KCNF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNF1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	2

Variants in KCNF1

This is a list of pathogenic ClinVar variants found in the KCNF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-10912434-G-A		not specified	Uncertain significance (Mar 07, 2024)
2-10912454-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-10912471-G-C		not specified	Uncertain significance (Oct 04, 2022)
2-10912674-C-T		Malignant tumor of prostate	Uncertain significance (-)
2-10912726-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-10912823-G-A		not specified	Uncertain significance (May 31, 2023)
2-10912832-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-10912892-G-A		not specified	Uncertain significance (Apr 07, 2023)
2-10912894-A-G			Benign (Jun 18, 2020)
2-10912911-G-A		not specified	Uncertain significance (Apr 07, 2023)
2-10912913-C-A		not specified	Uncertain significance (Dec 16, 2023)
2-10912964-C-T		not specified	Uncertain significance (Nov 12, 2021)
2-10913006-G-A		not specified	Likely benign (Apr 07, 2023)
2-10913029-G-A		not specified	Uncertain significance (May 30, 2024)
2-10913271-T-C		Moyamoya angiopathy	Likely pathogenic (-)
2-10913614-C-T			Benign (Oct 03, 2019)
2-10913756-G-A		not specified	Uncertain significance (Aug 22, 2023)
2-10913796-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-10913826-G-A		not specified	Uncertain significance (Jan 17, 2024)
2-10913871-A-G		not specified	Uncertain significance (Jun 10, 2024)
2-10913883-A-G		not specified	Uncertain significance (Jun 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNF1	protein_coding	protein_coding	ENST00000295082	1	2288

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.246	0.748	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.38	160	334	0.479	0.0000229	3205
Missense in Polyphen		29	146.98	0.19731		1448
Synonymous	0.975	147	163	0.903	0.0000129	1005
Loss of Function	2.37	3	11.8	0.254	5.05e-7	136

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative voltage-gated potassium channel.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.312
• hipred: Y
• hipred_score: 0.719
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnf1

Gene ontology

• Biological process: potassium ion transport;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;potassium channel activity