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LRRC42 leucine rich repeat containing 42 [ Homo sapiens (human) ]

Gene ID: 115353, updated on 5-Mar-2024

Summary

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Official Symbol
LRRC42provided by HGNC
Official Full Name
leucine rich repeat containing 42provided by HGNC
Primary source
HGNC:HGNC:28792
See related
Ensembl:ENSG00000116212 AllianceGenome:HGNC:28792
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
dJ167A19.4
Expression
Ubiquitous expression in thyroid (RPKM 11.3), testis (RPKM 10.8) and 25 other tissues See more
Orthologs
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Genomic context

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See LRRC42 in Genome Data Viewer
Location:
1p32.3
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53946350..53968168)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53829258..53851077)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54412023..54433841)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904180 Neighboring gene iodothyronine deiodinase 1 Neighboring gene uncharacterized LOC124904181 Neighboring gene intraflagellar transport 25 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 913 Neighboring gene Sharpr-MPRA regulatory region 3629 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:54422389-54423588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54424449-54425155 Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 12 Neighboring gene low density lipoprotein receptor class A domain containing 1

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. Identification of a nuclear protein, LRRC42, involved in lung carcinogenesis. Fujitomo T, et al. Int J Oncol, 2014 Jul. PMID 24806090
  2. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. Pech MF, et al. Elife, 2019 Aug 27. PMID 31452512, Free PMC Article
  3. ARIH2 Is a Vif-Dependent Regulator of CUL5-Mediated APOBEC3G Degradation in HIV Infection. Hüttenhain R, et al. Cell Host Microbe, 2019 Jul 10. PMID 31253590, Free PMC Article
  4. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743
  5. New interaction partners for Nek4.1 and Nek4.2 isoforms: from the DNA damage response to RNA splicing. Basei FL, et al. Proteome Sci, 2015. PMID 25798074, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

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)

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

  • MGC8974

General protein information

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Preferred Names
leucine-rich repeat-containing protein 42

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_001256409.2 → NP_001243338.1  leucine-rich repeat-containing protein 42

    See identical proteins and their annotated locations for NP_001243338.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK095767, CB851494, CX783955
    Consensus CDS
    CCDS585.1
    UniProtKB/Swiss-Prot
    D3DQ46, Q8N2Q8, Q9Y546
    Related
    ENSP00000360421.3, ENST00000371370.8
    Conserved Domains (2) summary
    sd00034
    Location:175 → 202
    LRR_AMN1; leucine-rich repeat [structural motif]
    cl26161
    Location:167 → 272
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

  2. NM_052940.5 → NP_443172.1  leucine-rich repeat-containing protein 42

    See identical proteins and their annotated locations for NP_443172.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK075201, CB851494, CX783955
    Consensus CDS
    CCDS585.1
    UniProtKB/Swiss-Prot
    D3DQ46, Q8N2Q8, Q9Y546
    Related
    ENSP00000318185.4, ENST00000319223.8
    Conserved Domains (2) summary
    sd00034
    Location:175 → 202
    LRR_AMN1; leucine-rich repeat [structural motif]
    cl26161
    Location:167 → 272
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    53946350..53968168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710328.5 → XP_006710391.1  leucine-rich repeat-containing protein 42 isoform X1

    See identical proteins and their annotated locations for XP_006710391.1

    UniProtKB/Swiss-Prot
    D3DQ46, Q8N2Q8, Q9Y546
    Conserved Domains (2) summary
    sd00034
    Location:175 → 202
    LRR_AMN1; leucine-rich repeat [structural motif]
    cl26161
    Location:167 → 272
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    53829258..53851077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334161.1 → XP_054190136.1  leucine-rich repeat-containing protein 42 isoform X1

    UniProtKB/Swiss-Prot
    D3DQ46, Q8N2Q8, Q9Y546

  2. XM_054334162.1 → XP_054190137.1  leucine-rich repeat-containing protein 42 isoform X1

    UniProtKB/Swiss-Prot
    D3DQ46, Q8N2Q8, Q9Y546
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y546.1 GenPept UniProtKB/Swiss-Prot:Q9Y546

Gene LinkOut

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