KCMF1

potassium channel modulatory factor 1, the group of Zinc fingers ZZ-type

Basic information

Region (hg38): 2:84971092-85059472

Links

ENSG00000176407 ∙ NCBI:56888 ∙ OMIM:614719 ∙ HGNC:20589 ∙ Uniprot:Q9P0J7 ∙ 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 KCMF1 gene.

• Inborn genetic diseases (4 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCMF1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	2

Variants in KCMF1

This is a list of pathogenic ClinVar variants found in the KCMF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85027930-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-85027988-G-C		not specified	Uncertain significance (Jan 05, 2022)
2-85049523-C-T			Benign (Sep 19, 2018)
2-85049531-G-A		not specified	Uncertain significance (Feb 28, 2024)
2-85049548-A-G		not specified	Uncertain significance (May 23, 2023)
2-85053210-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-85053283-T-C			Benign (Nov 06, 2018)
2-85053393-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-85053402-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCMF1	protein_coding	protein_coding	ENST00000409785	7	88380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0228	124590	0	2	124592	0.00000803

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.68	113	227	0.499	0.0000135	2474
Missense in Polyphen		34	90.915	0.37398		910
Synonymous	1.74	57	76.4	0.746	0.00000433	759
Loss of Function	3.48	1	16.0	0.0625	7.36e-7	210

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)	0.0000372	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has intrinsic E3 ubiquitin ligase activity and promotes ubiquitination. {ECO:0000269|PubMed:15581609}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0923

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.728
• ghis: 0.588

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcmf1
• Phenotype: neoplasm; endocrine/exocrine gland 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)

Gene ontology

• Biological process: protein ubiquitination;neutrophil degranulation
• Cellular component: extracellular region;cytosol;ficolin-1-rich granule lumen
• Molecular function: nucleic acid binding;zinc ion binding;ubiquitin protein ligase activity