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LRCH3 leucine rich repeats and calponin homology domain containing 3 [ Homo sapiens (human) ]

Gene ID: 84859, updated on 7-Apr-2024

Summary

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Official Symbol
LRCH3provided by HGNC
Official Full Name
leucine rich repeats and calponin homology domain containing 3provided by HGNC
Primary source
HGNC:HGNC:28637
See related
Ensembl:ENSG00000186001 AllianceGenome:HGNC:28637
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
Summary
Involved in septin cytoskeleton organization. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 3.8), lymph node (RPKM 3.6) and 25 other tissues See more
Orthologs
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Genomic context

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See LRCH3 in Genome Data Viewer
Location:
3q29
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (197791226..197888436)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (200523608..200620895)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (197518097..197615307)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene rubicon autophagy regulator Neighboring gene microRNA 922 Neighboring gene MPRA-validated peak4996 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21112 Neighboring gene Sharpr-MPRA regulatory region 8415 Neighboring gene Sharpr-MPRA regulatory region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197463053-197463900 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197466398-197466530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15092 Neighboring gene forty-two-three domain containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:197504526-197504699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21116 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197517785-197518499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21120 Neighboring gene uncharacterized LOC124909482 Neighboring gene uncharacterized LOC105374310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21121 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:197581553-197582752 Neighboring gene ribosomal protein L17 pseudogene 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197594026-197594561 Neighboring gene NUP98-IQCG recombination region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:197626412-197627184 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:197628168-197628668 Neighboring gene uncharacterized LOC124906330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15094 Neighboring gene RNA, U6 small nuclear 858, pseudogene Neighboring gene IQ motif containing G

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. LRCH proteins: a novel family of cytoskeletal regulators. Foussard H, et al. PLoS One, 2010 Aug 18. PMID 20805893, Free PMC Article
  2. DDX39B drives colorectal cancer progression by promoting the stability and nuclear translocation of PKM2. Zhao G, et al. Signal Transduct Target Ther, 2022 Aug 17. PMID 35973989, Free PMC Article
  3. DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169. Menon VR, et al. Cell Cycle, 2019 Mar. PMID 30773093, Free PMC Article
  4. 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
  5. Targeting RICTOR Sensitizes SMAD4-Negative Colon Cancer to Irinotecan. Wong CK, et al. Mol Cancer Res, 2020 Mar. PMID 31932471, Free PMC Article

See all (49) 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

  • MGC4126, FLJ20994, FLJ43245, FLJ44976

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 septin cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IC
Inferred by Curator
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
DISP complex protein LRCH3
Names
leucine-rich repeat and calponin homology domain-containing protein 3
leucine-rich repeats and calponin homology (CH) domain containing 3

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_001363887.1 → NP_001350816.1  DISP complex protein LRCH3 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC055764, AC135893, AC144530
    Consensus CDS
    CCDS87193.1
    UniProtKB/TrEMBL
    B4DEQ7
    Related
    ENSP00000394763.2, ENST00000428136.2
    Conserved Domains (3) summary
    smart00033
    Location:660 → 762
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  2. NM_001365715.1 → NP_001352644.1  DISP complex protein LRCH3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC055764, AC135893, AC144530
    Consensus CDS
    CCDS93456.1
    UniProtKB/Swiss-Prot
    B4E0T7, Q96FP9, Q96II8, Q9NT52
    UniProtKB/TrEMBL
    B4DEQ7
    Related
    ENSP00000393579.2, ENST00000425562.7
    Conserved Domains (3) summary
    smart00033
    Location:660 → 734
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  3. NM_001365716.1 → NP_001352645.1  DISP complex protein LRCH3 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC055764, AC135893, AC144530
    UniProtKB/TrEMBL
    B4DEQ7
    Conserved Domains (3) summary
    smart00033
    Location:624 → 726
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  4. NM_001365717.1 → NP_001352646.1  DISP complex protein LRCH3 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC055764, AC135893, AC144530
    UniProtKB/TrEMBL
    B4DEQ7
    Conserved Domains (3) summary
    smart00033
    Location:636 → 710
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  5. NM_001365718.1 → NP_001352647.1  DISP complex protein LRCH3 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC055764, AC135893, AC144530
    UniProtKB/TrEMBL
    B4DEQ7
    Conserved Domains (3) summary
    smart00033
    Location:624 → 698
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  6. NM_001365719.2 → NP_001352648.1  DISP complex protein LRCH3 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC055764, AC144530
    Conserved Domains (2) summary
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  7. NM_032773.4 → NP_116162.1  DISP complex protein LRCH3 isoform 2

    See identical proteins and their annotated locations for NP_116162.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK300466, BC007504, DB454969
    Consensus CDS
    CCDS3330.1
    UniProtKB/TrEMBL
    B4DEQ7
    Related
    ENSP00000334375.4, ENST00000334859.8
    Conserved Domains (3) summary
    smart00033
    Location:660 → 708
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

RNA

  1. NR_158582.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC055764, AC135893, AC144530

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    197791226..197888436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269367.4 → XP_005269424.1  DISP complex protein LRCH3 isoform X1

    UniProtKB/TrEMBL
    B4DEQ7
    Conserved Domains (3) summary
    smart00033
    Location:600 → 702
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  2. XM_047449082.1 → XP_047305038.1  DISP complex protein LRCH3 isoform X4

  3. XM_047449081.1 → XP_047305037.1  DISP complex protein LRCH3 isoform X2

  4. XM_017007352.3 → XP_016862841.1  DISP complex protein LRCH3 isoform X3

    UniProtKB/TrEMBL
    B4DEQ7
    Conserved Domains (4) summary
    smart00033
    Location:582 → 684
    CH; Calponin homology domain
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]
    pfam05917
    Location:427 → 590
    DUF874; Helicobacter pylori protein of unknown function (DUF874)

  5. XM_047449083.1 → XP_047305039.1  DISP complex protein LRCH3 isoform X5

  6. XM_011513242.4 → XP_011511544.1  DISP complex protein LRCH3 isoform X6

    Conserved Domains (2) summary
    COG4886
    Location:77 → 285
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:61 → 83
    LRR_RI; leucine-rich repeat [structural motif]

  7. XM_047449084.1 → XP_047305040.1  DISP complex protein LRCH3 isoform X7

RNA

  1. XR_007095758.1 RNA Sequence

  2. XR_007095759.1 RNA Sequence

  3. XR_007095760.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    200523608..200620895
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348135.1 → XP_054204110.1  DISP complex protein LRCH3 isoform X1

  2. XM_054348138.1 → XP_054204113.1  DISP complex protein LRCH3 isoform X4

  3. XM_054348136.1 → XP_054204111.1  DISP complex protein LRCH3 isoform X2

  4. XM_054348137.1 → XP_054204112.1  DISP complex protein LRCH3 isoform X3

  5. XM_054348139.1 → XP_054204114.1  DISP complex protein LRCH3 isoform X5

  6. XM_054348140.1 → XP_054204115.1  DISP complex protein LRCH3 isoform X6

  7. XM_054348141.1 → XP_054204116.1  DISP complex protein LRCH3 isoform X7

RNA

  1. XR_008486846.1 RNA Sequence

  2. XR_008486844.1 RNA Sequence

  3. XR_008486845.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96II8.2 GenPept UniProtKB/Swiss-Prot:Q96II8

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