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CHM CHM Rab escort protein [ Homo sapiens (human) ]

Gene ID: 1121, updated on 27-Nov-2024

Summary

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Official Symbol
CHMprovided by HGNC
Official Full Name
CHM Rab escort proteinprovided by HGNC
Primary source
HGNC:HGNC:1940
See related
Ensembl:ENSG00000188419 MIM:300390; AllianceGenome:HGNC:1940
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
TCD; GGTA; REP-1; DXS540; HSD-32
Summary
This gene encodes component A of the RAB geranylgeranyl transferase holoenzyme. In the dimeric holoenzyme, this subunit binds unprenylated Rab GTPases and then presents them to the catalytic Rab GGTase subunit for the geranylgeranyl transfer reaction. Rab GTPases need to be geranylgeranyled on either one or two cysteine residues in their C-terminus to localize to the correct intracellular membrane. Mutations in this gene are a cause of choroideremia; also known as tapetochoroidal dystrophy (TCD). This X-linked disease is characterized by progressive dystrophy of the choroid, retinal pigment epithelium and retina. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]
Expression
Ubiquitous expression in brain (RPKM 4.7), thyroid (RPKM 4.5) and 25 other tissues See more
Orthologs
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Genomic context

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See CHM in Genome Data Viewer
Location:
Xq21.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (85861180..86047558, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (84292297..84478778, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (85116185..85302562, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene microRNA 1321 Neighboring gene SFR1 pseudogene 2 Neighboring gene microRNA 361 Neighboring gene MPRA-validated peak7401 silencer Neighboring gene MPRA-validated peak7402 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:85257530-85258040 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:85270410-85271332 Neighboring gene NADH:ubiquinone oxidoreductase subunit A5 pseudogene 7 Neighboring gene stress induced phosphoprotein 1 pseudogene 3

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. Molecular analysis of the choroideremia gene related clinical findings in two families with choroideremia. Lin Y, et al. Mol Vis, 2011. PMID 22025891, Free PMC Article
  2. Rab geranylgeranylation occurs preferentially via the pre-formed REP-RGGT complex and is regulated by geranylgeranyl pyrophosphate. Baron RA, et al. Biochem J, 2008 Oct 1. PMID 18532927
  3. A novel mutation (967-970+2)delAAAGGT in the choroideremia gene found in a Japanese family and related clinical findings. Iino Y, et al. Jpn J Ophthalmol, 2008 Jul-Aug. PMID 18773267
  4. Fundus autofluorescence in carriers of choroideremia and correlation with electrophysiologic and psychophysical data. Preising MN, et al. Ophthalmology, 2009 Jun. PMID 19376587
  5. Choroideremia: new findings from ocular pathology and review of recent literature. MacDonald IM, et al. Surv Ophthalmol, 2009 May-Jun. PMID 19422966, Free PMC Article

See all (113) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of REP1 impacts choroidal melanogenesis and vasculogenesis in choroideremia.
    Title: Loss of REP1 impacts choroidal melanogenesis and vasculogenesis in choroideremia.
  2. Evaluation of CRISPR/Cas9 exon-skipping vector for choroideremia using human induced pluripotent stem cell-derived RPE.
    Title: Evaluation of CRISPR/Cas9 exon-skipping vector for choroideremia using human induced pluripotent stem cell-derived RPE.
  3. CHM mutation spectrum and disease: An update at the time of human therapeutic trials.
    Title: CHM mutation spectrum and disease: An update at the time of human therapeutic trials.
  4. REP1 deficiency causes systemic dysfunction of lipid metabolism and oxidative stress in choroideremia.
    Title: REP1 deficiency causes systemic dysfunction of lipid metabolism and oxidative stress in choroideremia.
  5. Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of CHM Gene Transcription.
    Title: Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of CHM Gene Transcription.
  6. Whole-exome sequencing identified a novel mutation in CHM of a Chinese family.
    Title: Whole-exome sequencing identified a novel mutation in CHM of a Chinese family.
  7. CLINICAL CHARACTERISTICS AND MOLECULAR GENETIC ANALYSIS OF A COHORT OF CHINESE PATIENTS WITH CHOROIDEREMIA.
    Title: CLINICAL CHARACTERISTICS AND MOLECULAR GENETIC ANALYSIS OF A COHORT OF CHINESE PATIENTS WITH CHOROIDEREMIA.
  8. Autofluorescence in female carriers with choroideremia: A familial case with a novel mutation in the CHM gene.
    Title: Autofluorescence in female carriers with choroideremia: A familial case with a novel mutation in the CHM gene.
  9. Next-generation sequencing-based clinical diagnosis of choroideremia and comprehensive mutational and clinical analyses.
    Title: Next-generation sequencing-based clinical diagnosis of choroideremia and comprehensive mutational and clinical analyses.
  10. Whole exome sequencing of a family revealed a novel variant in the CHM gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia.
    Title: Whole exome sequencing of a family revealed a novel variant in the CHM gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia.
Submit: New GeneRIF Correction See all GeneRIFs (64)

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

Associated conditions

Description Tests
Choroideremia
MedGen: C0008525 OMIM: 303100 GeneReviews: Choroideremia
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-03-24)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-03-24)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-Wide Association Study of Primary Dentition Pit-and-Fissure and Smooth Surface Caries.
EBI GWAS Catalog
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ38564, MGC102710

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GDP-dissociation inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
enables GTPase activator activity IEA
Inferred from Electronic Annotation
more info
  
enables Rab geranylgeranyltransferase activity TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in protein geranylgeranylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein targeting to membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in small GTPase-mediated signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of Rab-protein geranylgeranyltransferase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Rab-protein geranylgeranyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
rab proteins geranylgeranyltransferase component A 1
Names
CHM, Rab escort protein 1
choroideremia (Rab escort protein 1)

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_009874.2 RefSeqGene

    Range
    5001..191383
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_699

mRNA and Protein(s)

  1. NM_000390.4 → NP_000381.1  rab proteins geranylgeranyltransferase component A 1 isoform a

    See identical proteins and their annotated locations for NP_000381.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK291160, AL022401, BU688880, X78121
    Consensus CDS
    CCDS14454.1
    UniProtKB/Swiss-Prot
    A1L4D2, O43732, P24386
    UniProtKB/TrEMBL
    A8K545
    Related
    ENSP00000350386.2, ENST00000357749.7
    Conserved Domains (2) summary
    pfam13450
    Location:13 → 54
    NAD_binding_8; NAD(P)-binding Rossmann-like domain
    cl21454
    Location:225 → 542
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  2. NM_001145414.4 → NP_001138886.1  rab proteins geranylgeranyltransferase component A 1 isoform b

    See identical proteins and their annotated locations for NP_001138886.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a novel 3' terminal exon and lacks many exons at the 3' end compared to variant 1. The resulting isoform (b) is shorter with a distinct C-terminus compared to isoform a.
    Source sequence(s)
    BC032237, DB231066
    Consensus CDS
    CCDS48139.1
    UniProtKB/Swiss-Prot
    P24386
    Related
    ENSP00000484306.1, ENST00000615443.1
    Conserved Domains (1) summary
    cl21454
    Location:5 → 61
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  3. NM_001320959.1 → NP_001307888.1  rab proteins geranylgeranyltransferase component A 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' terminal exon, which results in translation initiation at an in-frame downstream start codon compared to variant 1. The resulting isoform (c) has a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AK291160, AL022401, BU688880, DA403806, X78121
    UniProtKB/TrEMBL
    B4DRL9
    Conserved Domains (1) summary
    cl21454
    Location:77 → 394
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  4. NM_001362517.1 → NP_001349446.1  rab proteins geranylgeranyltransferase component A 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' terminal exon, which results in translation initiation at an in-frame downstream start codon compared to variant 1. The resulting isoform (c) has a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AL009175, AL022401, AL035451
    UniProtKB/TrEMBL
    B4DRL9
    Conserved Domains (1) summary
    cl21454
    Location:77 → 394
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  5. NM_001362518.2 → NP_001349447.1  rab proteins geranylgeranyltransferase component A 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon and 5' splice site, which results in translation initiation at an in-frame downstream start codon compared to variant 1. The resulting isoform (c) has a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AL009175, AL022401, AL035451
    UniProtKB/TrEMBL
    B4DRL9
    Conserved Domains (1) summary
    cl21454
    Location:77 → 394
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  6. NM_001362519.1 → NP_001349448.1  rab proteins geranylgeranyltransferase component A 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' terminal exon and 5' splice site, which results in translation initiation at an in-frame downstream start codon compared to variant 1. The resulting isoform (c) has a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AL009175, AL022401, AL035451
    UniProtKB/TrEMBL
    B4DRL9
    Conserved Domains (1) summary
    cl21454
    Location:77 → 394
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    85861180..86047558 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047441793.1 → XP_047297749.1  rab proteins geranylgeranyltransferase component A 1 isoform X2

    UniProtKB/TrEMBL
    B4DRL9

  2. XM_047441794.1 → XP_047297750.1  rab proteins geranylgeranyltransferase component A 1 isoform X2

    UniProtKB/TrEMBL
    B4DRL9

  3. XM_017029242.3 → XP_016884731.1  rab proteins geranylgeranyltransferase component A 1 isoform X1

    UniProtKB/TrEMBL
    A8K545

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    84292297..84478778 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326408.1 → XP_054182383.1  rab proteins geranylgeranyltransferase component A 1 isoform X2

    UniProtKB/TrEMBL
    B4DRL9

  2. XM_054326409.1 → XP_054182384.1  rab proteins geranylgeranyltransferase component A 1 isoform X2

    UniProtKB/TrEMBL
    B4DRL9

  3. XM_054326407.1 → XP_054182382.1  rab proteins geranylgeranyltransferase component A 1 isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001037312.1: Suppressed sequence

    Description
    NM_001037312.1: This RefSeq was permanently suppressed because the alternate 3'UTR represented is supported by few transcripts and the resulting protein is significantly truncated.

  2. NM_152579.2: Suppressed sequence

    Description
    NM_152579.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P24386.3 GenPept UniProtKB/Swiss-Prot:P24386

Gene LinkOut

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