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KLHL42 kelch like family member 42 [ Homo sapiens (human) ]

Gene ID: 57542, updated on 5-Mar-2024

Summary

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Official Symbol
KLHL42provided by HGNC
Official Full Name
kelch like family member 42provided by HGNC
Primary source
HGNC:HGNC:29252
See related
Ensembl:ENSG00000087448 MIM:618919; AllianceGenome:HGNC:29252
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
Ctb9; KLHDC5
Summary
Contributes to ubiquitin-protein transferase activity. Involved in proteasome-mediated ubiquitin-dependent protein catabolic process; protein polyubiquitination; and regulation of microtubule-based process. Part of Cul3-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 7.6), endometrium (RPKM 5.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
12p11.22
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (27780233..27803040)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (27651947..27674765)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (27933166..27955973)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MRPS35 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:27857921-27858432 Neighboring gene high mobility group box 1 pseudogene 49 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6149 Neighboring gene mitochondrial ribosomal protein S35 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:27904053-27904827 Neighboring gene MANSC domain containing 4 Neighboring gene MPRA-validated peak1632 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4313 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:27933183-27933682 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27127 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_27159 Neighboring gene uncharacterized LOC105369709 Neighboring gene RN7SK pseudogene 15 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:27974511-27975710

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
  • 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. Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis. Lear TB, et al. J Biol Chem, 2020 Mar 27. PMID 32071084, Free PMC Article
  2. The Cul3/Klhdc5 E3 ligase regulates p60/katanin and is required for normal mitosis in mammalian cells. Cummings CM, et al. J Biol Chem, 2009 Apr 24. PMID 19261606, Free PMC Article
  3. The ubiquitin conjugating enzyme, UbcM2, engages in novel interactions with components of cullin-3 based E3 ligases. Plafker KS, et al. Biochemistry, 2009 Apr 21. PMID 19256485, Free PMC Article
  4. A novel missense variant in CUL3 shows altered binding ability to BTB-adaptor proteins leading to diverse phenotypes of CUL3-related disorders. Kato K, et al. J Hum Genet, 2021 May. PMID 33130828
  5. Novel Cul3 binding proteins function to remodel E3 ligase complexes. Wimuttisuk W, et al. BMC Cell Biol, 2014 Jul 10. PMID 25011449, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis.
    Title: Kelch-like protein 42 is a profibrotic ubiquitin E3 ligase involved in systemic sclerosis.
  2. Cul3-deficient cells or Ctb9/KLHDC5-deficient cells show an increase in p60/katanin levels, indicating that Cul3/Ctb9/KLHDC5 is required for efficient p60/katanin removal
    Title: The Cul3/Klhdc5 E3 ligase regulates p60/katanin and is required for normal mitosis in mammalian cells.
Submit: New GeneRIF Correction

Phenotypes

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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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1340, MGC131714

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein polyubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of microtubule-based process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of microtubule-based process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Cul3-RING ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Cul3-RING ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in spindle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
kelch-like protein 42
Names
cullin-3-binding protein 9
kelch domain containing 5
kelch domain-containing protein 5

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_020782.2 → NP_065833.1  kelch-like protein 42

    See identical proteins and their annotated locations for NP_065833.1

    Status: VALIDATED

    Source sequence(s)
    AC009511
    Consensus CDS
    CCDS31763.1
    UniProtKB/Swiss-Prot
    Q2VPK1, Q8N334, Q9P2K6
    UniProtKB/TrEMBL
    B2RNT7
    Related
    ENSP00000370671.2, ENST00000381271.7
    Conserved Domains (4) summary
    PHA03098
    Location:210 → 497
    PHA03098; kelch-like protein; Provisional
    sd00038
    Location:244 → 287
    Kelch; KELCH repeat [structural motif]
    cd18319
    Location:4 → 111
    BTB_POZ_KLHL42; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 42 (KLHL42)
    cd18478
    Location:128 → 237
    BACK_KLHL42_KLHDC5; BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 42 (KLHL42)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    27780233..27803040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019698.3 → XP_016875187.1  kelch-like protein 42 isoform X1

    UniProtKB/TrEMBL
    F5H523
    Related
    ENSP00000444748.1, ENST00000539176.1
    Conserved Domains (4) summary
    cd14735
    Location:129 → 169
    BACK_Kelch; BTB-And-C-terminal-Kelch (BACK) domain of Kelch-like proteins
    sd00038
    Location:244 → 287
    Kelch; KELCH repeat [structural motif]
    cl02518
    Location:7 → 69
    BTB; BTB/POZ domain
    cl28614
    Location:217 → 353
    BTB; Broad-Complex, Tramtrack and Bric a brac

RNA

  1. XR_931315.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    27651947..27674765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372646.1 → XP_054228621.1  kelch-like protein 42 isoform X1

    UniProtKB/TrEMBL
    F5H523

RNA

  1. XR_008488645.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P2K6.2 GenPept UniProtKB/Swiss-Prot:Q9P2K6

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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