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

    Gene ID: 1121, updated on 10-Dec-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
    mouse all
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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 variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

      UniProtKB/TrEMBL
      A8K545

    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 info@ncbi.nlm.nih.gov 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

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

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