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KCMF1 potassium channel modulatory factor 1 [ Homo sapiens (human) ]

Gene ID: 56888, updated on 2-Nov-2024

Summary

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Official Symbol
KCMF1provided by HGNC
Official Full Name
potassium channel modulatory factor 1provided by HGNC
Primary source
HGNC:HGNC:20589
See related
Ensembl:ENSG00000176407 MIM:614719; AllianceGenome:HGNC:20589
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FIGC; PCMF; ZZZ1; DEBT91
Summary
Enables ubiquitin protein ligase activity. Involved in several processes, including negative regulation of HRI-mediated signaling; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein polyubiquitination. Located in cytosol. Is active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 9.7), thyroid (RPKM 7.1) and 25 other tissues See more
Orthologs
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Genomic context

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See KCMF1 in Genome Data Viewer
Location:
2p11.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (84971161..85059472)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (84972983..85061380)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (85198284..85286595)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374836 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11689 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:85133043-85134242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11690 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:85146489-85147688 Neighboring gene thymosin beta 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85153187-85153848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16109 Neighboring gene ribosomal protein S2 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16111 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16113 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85184893-85185581 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85185582-85186272 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85186273-85186962 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:85186963-85187652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85201557-85202098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85202099-85202640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85250397-85251081 Neighboring gene long intergenic non-protein coding RNA 1964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85304907-85305408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:85305409-85305908 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. KCMF1 regulates autophagy and ion channels' function in renal cell carcinoma: a future therapeutic target. Singh A, et al. J Cancer Res Clin Oncol, 2023 Aug. PMID 36515749
  2. Suppression of KCMF1 by constitutive high CD99 expression is involved in the migratory ability of Ewing's sarcoma cells. Kreppel M, et al. Oncogene, 2006 May 4. PMID 16314831
  3. Genome-wide CRISPR Analysis Identifies Substrate-Specific Conjugation Modules in ER-Associated Degradation. Leto DE, et al. Mol Cell, 2019 Jan 17. PMID 30581143, Free PMC Article
  4. MicroRNA-210 contributes to preeclampsia by downregulating potassium channel modulatory factor 1. Luo R, et al. Hypertension, 2014 Oct. PMID 24980667
  5. FIGC, a novel FGF-induced ubiquitin-protein ligase in gastric cancers. Jang JH. FEBS Lett, 2004 Dec 3. PMID 15581609

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KCMF1 regulates autophagy and ion channels' function in renal cell carcinoma: a future therapeutic target.
    Title: KCMF1 regulates autophagy and ion channels' function in renal cell carcinoma: a future therapeutic target.
  2. CircHIPK3 contributes to human villous trophoblast growth, migration and invasion via modulating the pathway of miR-346/KCMF1.
    Title: CircHIPK3 contributes to human villous trophoblast growth, migration and invasion via modulating the pathway of miR-346/KCMF1.
  3. Results showed KCMF1 C-terminus binds directly to RAD6, whereas N-terminal domains interact with UBR4 and point mutations found in X-linked intellectual disability (XLID) patients specifically lose the interaction with KCMF1 and UBR4.
    Title: KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation.
  4. Data indicate that expressions of miR-210 and potassium channel modulatory factor 1 (KCMF1) exhibited an inverse correlation in placentas from patients with severe preeclampsia.
    Title: MicroRNA-210 contributes to preeclampsia by downregulating potassium channel modulatory factor 1.
  5. Data indicate that FIGC upregulation in response to basic fibroblast growth factor in gastric cancer might be implicated in carcinogenesis through dysregulation of growth modulator.
    Title: FIGC, a novel FGF-induced ubiquitin-protein ligase in gastric cancers.
  6. Suppression of KCMF1 by constitutive high CD99 expression levels contribute to the malignant properties of Ewing's sarcoma by promoting growth and migration of tumor cells
    Title: Suppression of KCMF1 by constitutive high CD99 expression is involved in the migratory ability of Ewing's sarcoma cells.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp434L1021

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in negative regulation of HRI-mediated signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein K63-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to oxidative stress IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in synaptic signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
  
located_in late endosome IEA
Inferred from Electronic Annotation
more info
  
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
E3 ubiquitin-protein ligase KCMF1
Names
FGF-induced in gastric cancer
FGF-induced ubiquitin-protein ligase in gastric cancers
RING-type E3 ubiquitin transferase KCMF1
ZZ-type zinc finger-containing protein 1
differentially expressed in branching tubulogenesis 91
zinc finger, ZZ domain containing 1
NP_064507.3
XP_006712115.1
XP_047301082.1
XP_054199024.1
XP_054199025.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_020122.5 → NP_064507.3  E3 ubiquitin-protein ligase KCMF1

    See identical proteins and their annotated locations for NP_064507.3

    Status: VALIDATED

    Source sequence(s)
    AC078974, AK023403, AW466865, CT004343
    Consensus CDS
    CCDS46350.1
    UniProtKB/Swiss-Prot
    Q4ZG04, Q53SC7, Q9BWK2, Q9H8P5, Q9P0J7, Q9UFE8
    Related
    ENSP00000386738.3, ENST00000409785.9
    Conserved Domains (2) summary
    cd02338
    Location:7 → 55
    ZZ_PCMF_like; Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel ...
    pfam05605
    Location:76 → 137
    zf-Di19; Drought induced 19 protein (Di19), zinc-binding

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    84971161..85059472
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047445126.1 → XP_047301082.1  E3 ubiquitin-protein ligase KCMF1 isoform X1

  2. XM_006712052.4 → XP_006712115.1  E3 ubiquitin-protein ligase KCMF1 isoform X2

    Conserved Domains (3) summary
    cd02338
    Location:15 → 63
    ZZ_PCMF_like; Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel ...
    pfam05605
    Location:84 → 145
    zf-Di19; Drought induced 19 protein (Di19), zinc-binding
    pfam14571
    Location:288 → 336
    Di19_C; Stress-induced protein Di19, C-terminal

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    84972983..85061380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343049.1 → XP_054199024.1  E3 ubiquitin-protein ligase KCMF1 isoform X1

  2. XM_054343050.1 → XP_054199025.1  E3 ubiquitin-protein ligase KCMF1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P0J7.2 GenPept UniProtKB/Swiss-Prot:Q9P0J7

Gene LinkOut

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