U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LRCH1 leucine rich repeats and calponin homology domain containing 1 [ Homo sapiens (human) ]

Gene ID: 23143, updated on 17-Jun-2024

Summary

Official Symbol
LRCH1provided by HGNC
Official Full Name
leucine rich repeats and calponin homology domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20309
See related
Ensembl:ENSG00000136141 MIM:610368; AllianceGenome:HGNC:20309
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
NP81; CHDC1
Summary
This gene encodes a protein with a leucine-rich repeat and a calponin homology domain. Polymorphism in this gene may be associated with susceptibililty to knee osteoarthritis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2010]
Expression
Ubiquitous expression in endometrium (RPKM 5.5), placenta (RPKM 5.5) and 25 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See LRCH1 in Genome Data Viewer
Location:
13q14.13-q14.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (46553170..46753041)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (45774368..45974291)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (47127305..47327176)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903171 Neighboring gene FKBP prolyl isomerase 1A pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5323 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:47127762-47128462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:47192746-47193250 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:47193251-47193753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7712 Neighboring gene uncharacterized LOC107984563 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:47370431-47371032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7713 Neighboring gene esterase D

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ41660, KIAA1016

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 cellular response to chemokine IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cellular response to chemokine IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of GTPase activity IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of T cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of T cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
leucine-rich repeat and calponin homology domain-containing protein 1
Names
leucine-rich repeats and calponin homology (CH) domain containing 1
neuronal protein 81

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_021335.2 RefSeqGene

    Range
    5002..196730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164211.2NP_001157683.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL136958, AL138704, AL359880
    Consensus CDS
    CCDS53865.1
    UniProtKB/TrEMBL
    A8KA33
    Related
    ENSP00000374447.3, ENST00000389797.8
    Conserved Domains (4) summary
    smart00033
    Location:615704
    CH; Calponin homology domain
    sd00033
    Location:7698
    LRR_RI; leucine-rich repeat [structural motif]
    cl26018
    Location:71274
    NEL; C-terminal novel E3 ligase, LRR-interacting
    cl26761
    Location:311513
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
  2. NM_001164213.2NP_001157685.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and uses an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR, compared to variant 1, and a shorter protein (isoform 3) with a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL136958, AL138704, AL359880
    Consensus CDS
    CCDS53866.1
    UniProtKB/TrEMBL
    A8KA33
    Related
    ENSP00000308493.5, ENST00000311191.10
    Conserved Domains (4) summary
    PRK15370
    Location:71274
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:580685
    CH; Calponin homology domain
    COG5271
    Location:311601
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    sd00033
    Location:7698
    LRR_RI; leucine-rich repeat [structural motif]
  3. NM_015116.3NP_055931.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AL136958, AL138704, AL359880
    Consensus CDS
    CCDS31972.1
    UniProtKB/Swiss-Prot
    B7ZLL5, F8W6F0, Q17R43, Q2KHR1, Q5TBU9, Q7Z5F6, Q7Z5F7, Q9Y2L9
    UniProtKB/TrEMBL
    A8KA33
    Related
    ENSP00000374448.3, ENST00000389798.7
    Conserved Domains (4) summary
    PRK15370
    Location:71274
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:580669
    CH; Calponin homology domain
    COG5271
    Location:311601
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    sd00033
    Location:7698
    LRR_RI; leucine-rich repeat [structural motif]

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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    46553170..46753041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020483.2XP_016875972.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A8KA33
  2. XM_047430214.1XP_047286170.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    45774368..45974291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374310.1XP_054230285.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    A8KA33
  2. XM_054374311.1XP_054230286.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2