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LRRC40 leucine rich repeat containing 40 [ Homo sapiens (human) ]

Gene ID: 55631, updated on 5-Mar-2024

Summary

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Official Symbol
LRRC40provided by HGNC
Official Full Name
leucine rich repeat containing 40provided by HGNC
Primary source
HGNC:HGNC:26004
See related
Ensembl:ENSG00000066557 AllianceGenome:HGNC:26004
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
dJ677H15.1
Summary
Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in signal transduction. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 8.0), testis (RPKM 8.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p31.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (70144805..70205579, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (70023294..70084095, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (70610488..70671262, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 7 Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 1 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70503542-70504181 Neighboring gene LRRC7 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:70534982-70535190 Neighboring gene Sharpr-MPRA regulatory region 9273 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70606447-70606948 Neighboring gene Sharpr-MPRA regulatory region 3760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:70626481-70626982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1187 Neighboring gene RNA, 7SL, cytoplasmic 242, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:70686957-70687502 Neighboring gene MPRA-validated peak281 silencer Neighboring gene serine and arginine rich splicing factor 11 Neighboring gene ankyrin repeat domain 13C Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:70818812-70820011 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:70820190-70821107

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. PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder. Pijuan J, et al. Autism Res, 2021 Jun. PMID 33749153
  2. Mass spectrometry-based proteomic analysis of FSCN1-interacting proteins in laryngeal squamous cell carcinoma cells. Liu H, et al. IUBMB Life, 2019 Nov. PMID 31298480
  3. STUB1 is targeted by the SUMO-interacting motif of EBNA1 to maintain Epstein-Barr Virus latency. Wang Y, et al. PLoS Pathog, 2020 Mar. PMID 32176739, Free PMC Article
  4. Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. Barbosa JAF, et al. J Virol, 2021 Jul 12. PMID 34011540, Free PMC Article
  5. UM171 Preserves Epigenetic Marks that Are Reduced in Ex Vivo Culture of Human HSCs via Potentiation of the CLR3-KBTBD4 Complex. Chagraoui J, et al. Cell Stem Cell, 2021 Jan 7. PMID 33417871

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder.
    Title: PLXNA2 and LRRC40 as candidate genes in autism spectrum disorder.
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)

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

  • FLJ20331

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in membrane HDA PubMed 

General protein information

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Preferred Names
leucine-rich repeat-containing protein 40
Names
testicular tissue protein Li 109

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_017768.5 → NP_060238.3  leucine-rich repeat-containing protein 40

    See identical proteins and their annotated locations for NP_060238.3

    Status: VALIDATED

    Source sequence(s)
    AI015897, BC008586, DA310461
    Consensus CDS
    CCDS646.1
    UniProtKB/Swiss-Prot
    Q9BTR7, Q9H9A6, Q9NSK1, Q9NXC1
    UniProtKB/TrEMBL
    A0A140VJN3
    Related
    ENSP00000359990.3, ENST00000370952.4
    Conserved Domains (3) summary
    sd00033
    Location:107 → 129
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:84 → 140
    LRR_8; Leucine rich repeat
    cl26793
    Location:120 → 577
    PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional

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
    70144805..70205579 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541763.2 → XP_011540065.1  leucine-rich repeat-containing protein 40 isoform X2

    See identical proteins and their annotated locations for XP_011540065.1

    Conserved Domains (3) summary
    PLN00113
    Location:1 → 359
    PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
    sd00031
    Location:302 → 325
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:27 → 48
    LRR_RI; leucine-rich repeat [structural motif]

  2. XM_047424520.1 → XP_047280476.1  leucine-rich repeat-containing protein 40 isoform X2

  3. XM_047424519.1 → XP_047280475.1  leucine-rich repeat-containing protein 40 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    70023294..70084095 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337542.1 → XP_054193517.1  leucine-rich repeat-containing protein 40 isoform X2

  2. XM_054337541.1 → XP_054193516.1  leucine-rich repeat-containing protein 40 isoform X2

  3. XM_054337540.1 → XP_054193515.1  leucine-rich repeat-containing protein 40 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H9A6.1 GenPept UniProtKB/Swiss-Prot:Q9H9A6

Gene LinkOut

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

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