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LRCH2 leucine rich repeats and calponin homology domain containing 2 [ Homo sapiens (human) ]

Gene ID: 57631, updated on 5-Mar-2024

Summary

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Official Symbol
LRCH2provided by HGNC
Official Full Name
leucine rich repeats and calponin homology domain containing 2provided by HGNC
Primary source
HGNC:HGNC:29292
See related
Ensembl:ENSG00000130224 AllianceGenome:HGNC:29292
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
dA204F4.4
Summary
This gene encodes a member of the leucine-rich repeat and calponin homology domain-containing protein family. These family members contain multiple N-terminal leucine-rich repeats, in addition to a C-terminal calponin homology domain, a type of domain that mediates interactions with actin filaments. These proteins are conserved across animal species, and studies of a similar Drosophila protein indicate a function as a cytoskeletal scaffolding protein. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2011]
Expression
Broad expression in prostate (RPKM 3.7), brain (RPKM 2.9) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
Xq23
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (115110616..115234096, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (113519325..113642681, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (114345179..114468659, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 670 pseudogene Neighboring gene YAP1 pseudogene 2 Neighboring gene small nucleolar RNA, H/ACA box 35B Neighboring gene TMSB4X pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:114424095-114424596 Neighboring gene RBMX like 3 Neighboring gene ribosomal protein L36 pseudogene 18 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:114552544-114553121 Neighboring gene leucine zipper protein 4 Neighboring gene uncharacterized LOC107985681 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:114579651-114580150 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:114606578-114607435 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:114607575-114608077

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. Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity. Ng A, et al. Autophagy, 2011 Sep. PMID 21606681, Free PMC Article
  2. Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Ng AC, et al. Proc Natl Acad Sci U S A, 2011 Mar 15. PMID 20616063, Free PMC Article
  3. LRCH proteins: a novel family of cytoskeletal regulators. Foussard H, et al. PLoS One, 2010 Aug 18. PMID 20805893, Free PMC Article
  4. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
  5. The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics. O'Loughlin T, et al. EMBO Rep, 2018 Apr. PMID 29467281, Free PMC Article

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

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

  • KIAA1495, MGC150671

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
leucine-rich repeat and calponin homology domain-containing protein 2
Names
leucine-rich repeats and calponin homology (CH) domain containing 2

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.

Genomic

  1. NG_021299.2 RefSeqGene

    Range
    4977..128457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243963.2 → NP_001230892.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AC239923, BC125224, BX647193
    Consensus CDS
    CCDS59175.1
    UniProtKB/Swiss-Prot
    Q5VUJ6
    Related
    ENSP00000439366.1, ENST00000538422.2
    Conserved Domains (5) summary
    cd00116
    Location:136 → 237
    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 ...
    sd00033
    Location:92 → 112
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00307
    Location:627 → 734
    CH; Calponin homology (CH) domain
    pfam12799
    Location:136 → 173
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:181 → 237
    LRR_8; Leucine rich repeat

  2. NM_020871.4 → NP_065922.3  leucine-rich repeat and calponin homology domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_065922.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB040928, AC239923, BG541540, BX647193
    Consensus CDS
    CCDS48155.1
    UniProtKB/Swiss-Prot
    F5H2T1, Q08AD5, Q5VUJ6, Q9HA88, Q9P233
    Related
    ENSP00000325091.8, ENST00000317135.13
    Conserved Domains (5) summary
    cd00116
    Location:136 → 237
    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 ...
    sd00033
    Location:92 → 112
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00307
    Location:644 → 751
    CH; Calponin homology (CH) domain
    pfam12799
    Location:136 → 173
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:181 → 237
    LRR_8; Leucine rich repeat

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    115110616..115234096 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006724724.4 → XP_006724787.2  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X1

    Conserved Domains (5) summary
    cd00116
    Location:136 → 237
    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 ...
    sd00033
    Location:92 → 112
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00307
    Location:637 → 744
    CH; Calponin homology (CH) domain
    pfam12799
    Location:136 → 173
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:181 → 237
    LRR_8; Leucine rich repeat

  2. XM_017029696.3 → XP_016885185.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    113519325..113642681 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327463.1 → XP_054183438.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X1

  2. XM_054327464.1 → XP_054183439.1  leucine-rich repeat and calponin homology domain-containing protein 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VUJ6.2 GenPept UniProtKB/Swiss-Prot:Q5VUJ6

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