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Aliases for CHM Gene

Aliases for CHM Gene

  • CHM, Rab Escort Protein 1 2 3
  • Choroideremia (Rab Escort Protein 1) 2 3 5
  • REP-1 3 4
  • TCD 3 4
  • Choroideremia Protein 4
  • Rab Escort Protein 1 4
  • TCD Protein 4
  • HSD-32 3
  • DXS540 3
  • GGTA 3
  • REP1 4

External Ids for CHM Gene

Previous HGNC Symbols for CHM Gene

  • TCD
  • DXS540

Previous GeneCards Identifiers for CHM Gene

  • GC0XM080499
  • GC0XM082196
  • GC0XM083152
  • GC0XM083889
  • GC0XM083891
  • GC0XM084923
  • GC0XM085002
  • GC0XM085116
  • GC0XM078692

Summaries for CHM Gene

Entrez Gene Summary for CHM Gene

  • 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]

GeneCards Summary for CHM Gene

CHM (CHM, Rab Escort Protein 1) is a Protein Coding gene. Diseases associated with CHM include choroideremia and charcot-marie-tooth disease, type 1b. Among its related pathways are Gene Expression and Regulation of TP53 Activity. GO annotations related to this gene include GTPase activator activity and Rab geranylgeranyltransferase activity. An important paralog of this gene is CHML.

UniProtKB/Swiss-Prot for CHM Gene

  • Substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B composed of RABGGTA and RABGGTB, and remains bound to it after the geranylgeranyl transfer reaction. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Besides, a pre-formed complex consisting of CHM and the Rab GGTase dimer (RGGT or component B) can bind to and prenylate Rab proteins; this alternative pathway is proposed to be the predominant pathway for Rab protein geranylgeranylation.

Gene Wiki entry for CHM Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHM Gene

Genomics for CHM Gene

Regulatory Elements for CHM Gene

Promoters for CHM Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around CHM on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the CHM gene promoter:

Genomic Location for CHM Gene

Chromosome:
X
Start:
85,861,180 bp from pter
End:
86,047,562 bp from pter
Size:
186,383 bases
Orientation:
Minus strand

Genomic View for CHM Gene

Genes around CHM on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CHM Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CHM Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CHM Gene

Proteins for CHM Gene

  • Protein details for CHM Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P24386-RAE1_HUMAN
    Recommended name:
    Rab proteins geranylgeranyltransferase component A 1
    Protein Accession:
    P24386
    Secondary Accessions:
    • A1L4D2
    • O43732

    Protein attributes for CHM Gene

    Size:
    653 amino acids
    Molecular mass:
    73476 Da
    Quaternary structure:
    • Monomer. Heterotrimer composed of RABGGTA, RABGGTB and CHM; within this trimer, RABGGTA and RABGGTB form the catalytic component B, while CHM (component A) mediates Rab protein binding. Can associate with the Rab GGTase dimer (RGGT or component B) prior to Rab protein binding; the association is stabilized by geranylgeranyl pyrophosphate (GGpp). The CHM:RGGT:Rab complex is destabilized by GGpp. Interacts with RAB1A, RAB1B, RAB5A, RAB7A and RAB27A and mediates their prenylation.

    Alternative splice isoforms for CHM Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CHM Gene

Proteomics data for CHM Gene at MOPED

Post-translational modifications for CHM Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CHM Gene

No data available for DME Specific Peptides for CHM Gene

Domains & Families for CHM Gene

Graphical View of Domain Structure for InterPro Entry

P24386

UniProtKB/Swiss-Prot:

RAE1_HUMAN :
  • Belongs to the Rab GDI family.
Family:
  • Belongs to the Rab GDI family.
genes like me logo Genes that share domains with CHM: view

No data available for Gene Families for CHM Gene

Function for CHM Gene

Molecular function for CHM Gene

UniProtKB/Swiss-Prot Function:
Substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B composed of RABGGTA and RABGGTB, and remains bound to it after the geranylgeranyl transfer reaction. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Besides, a pre-formed complex consisting of CHM and the Rab GGTase dimer (RGGT or component B) can bind to and prenylate Rab proteins; this alternative pathway is proposed to be the predominant pathway for Rab protein geranylgeranylation.

Gene Ontology (GO) - Molecular Function for CHM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with CHM: view
genes like me logo Genes that share phenotypes with CHM: view

Human Phenotype Ontology for CHM Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CHM Gene

MGI Knock Outs for CHM:

Animal Model Products

miRNA for CHM Gene

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CHM Gene

Localization for CHM Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHM Gene

Cytoplasm, cytosol.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CHM Gene COMPARTMENTS Subcellular localization image for CHM gene
Compartment Confidence
cytosol 5
nucleus 3
endoplasmic reticulum 2
extracellular 1
mitochondrion 1
peroxisome 1
plasma membrane 1

No data available for Gene Ontology (GO) - Cellular Components for CHM Gene

Pathways & Interactions for CHM Gene

genes like me logo Genes that share pathways with CHM: view

Gene Ontology (GO) - Biological Process for CHM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006612 protein targeting to membrane IMP 7957092
GO:0018344 protein geranylgeranylation IDA 7957092
GO:0050896 response to stimulus IEA --
genes like me logo Genes that share ontologies with CHM: view

No data available for SIGNOR curated interactions for CHM Gene

Drugs & Compounds for CHM Gene

(2) Drugs for CHM Gene - From: DrugBank and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FARNESYL Experimental Pharma Target 0

(6) Additional Compounds for CHM Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CHM: view

Transcripts for CHM Gene

Unigene Clusters for CHM Gene

Choroideremia (Rab escort protein 1):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CHM Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b
SP1: -
SP2: - -
SP3: - - -
SP4: -
SP5:
SP6: -

Relevant External Links for CHM Gene

GeneLoc Exon Structure for
CHM
ECgene alternative splicing isoforms for
CHM

Expression for CHM Gene

mRNA expression in normal human tissues for CHM Gene

Protein differential expression in normal tissues from HIPED for CHM Gene

This gene is overexpressed in Frontal cortex (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CHM Gene



SOURCE GeneReport for Unigene cluster for CHM Gene Hs.496449

genes like me logo Genes that share expression patterns with CHM: view

Protein tissue co-expression partners for CHM Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for CHM Gene

Orthologs for CHM Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CHM Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia CHM 35
  • 90.3 (n)
  • 88.21 (a)
CHM 36
  • 88 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CHM 35
  • 90.64 (n)
  • 88.34 (a)
CHM 36
  • 88 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Chm 35
  • 86.3 (n)
  • 84.39 (a)
Chm 16
Chm 36
  • 82 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CHM 35
  • 99.74 (n)
  • 99.54 (a)
CHM 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Chm 35
  • 86.4 (n)
  • 84.23 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 58 (a)
ManyToMany
-- 36
  • 71 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 54 (a)
ManyToMany
-- 36
  • 63 (a)
ManyToMany
chicken
(Gallus gallus)
Aves CHM 35
  • 69.98 (n)
  • 66.56 (a)
CHM 36
  • 65 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 64 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia chml 35
  • 63.88 (n)
  • 57.98 (a)
African clawed frog
(Xenopus laevis)
Amphibia MGC68578 35
zebrafish
(Danio rerio)
Actinopterygii Dr.17040 35
chm 36
  • 53 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.635 35
fruit fly
(Drosophila melanogaster)
Insecta Rep 37
  • 34 (a)
Rep 35
  • 46.41 (n)
  • 39.43 (a)
Rep 36
  • 36 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010419 35
  • 51.07 (n)
  • 42.95 (a)
worm
(Caenorhabditis elegans)
Secernentea Y67D2.1 37
  • 30 (a)
rep-1 36
  • 34 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GDI1 36
  • 24 (a)
OneToMany
Species with no ortholog for CHM:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CHM Gene

ENSEMBL:
Gene Tree for CHM (if available)
TreeFam:
Gene Tree for CHM (if available)

Paralogs for CHM Gene

Paralogs for CHM Gene

(2) SIMAP similar genes for CHM Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CHM: view

Variants for CHM Gene

Sequence variations from dbSNP and Humsavar for CHM Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
VAR_008273 Choroideremia (CHM)
VAR_066847 Choroideremia (CHM)
VAR_066848 Choroideremia (CHM)
rs1015148 -- 86,027,411(+) GTACA(A/G)ACATA intron-variant
rs1018368 -- 85,939,626(-) ATTCC(A/G)CACCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CHM Gene

Variant ID Type Subtype PubMed ID
esv2740276 CNV Deletion 23290073
nsv519786 CNV Gain 19592680
nsv438141 CNV Loss 16468122
esv2740277 CNV Deletion 23290073
nsv510545 CNV Loss 20534489

Variation tolerance for CHM Gene

Residual Variation Intolerance Score: 54.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.69; 46.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CHM Gene

HapMap Linkage Disequilibrium report
CHM
Human Gene Mutation Database (HGMD)
CHM

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CHM Gene

Disorders for CHM Gene

MalaCards: The human disease database

(13) MalaCards diseases for CHM Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
choroideremia
  • choroidal sclerosis
charcot-marie-tooth disease, type 1b
  • charcot-marie-tooth disease
charcot-marie-tooth disease, type 2j
  • charcot-marie-tooth disease type 2j
charcot-marie-tooth disease, type 2i
  • charcot-marie-tooth disease type 2i
charcot-marie-tooth disease, dominant intermediate d
  • cmtdid
- elite association - COSMIC cancer census association via MalaCards
Search CHM in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RAE1_HUMAN
  • Choroideremia (CHM) [MIM:303100]: An X-linked recessive disease characterized by a slowly progressive degeneration of the choroid, photoreceptors, and retinal pigment epithelium. Affected males develop night blindness in their teenage years followed by loss of peripheral vision and complete blindness at middle age. Carrier females are generally asymptomatic but funduscopic examination often shows patchy areas of chorioretinal atrophy. {ECO:0000269 PubMed:19427510, ECO:0000269 PubMed:21905166, ECO:0000269 PubMed:7951216}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for CHM Gene

choroideremia

Relevant External Links for CHM

Genetic Association Database (GAD)
CHM
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CHM
genes like me logo Genes that share disorders with CHM: view

Publications for CHM Gene

  1. The functional effect of pathogenic mutations in Rab escort protein 1. (PMID: 19427510) Sergeev Y.V. … Macdonald I.M. (Mutat. Res. 2009) 3 4 23 67
  2. Choroideremia: new findings from ocular pathology and review of recent literature. (PMID: 19422966) MacDonald I.M. … Chan C.C. (Surv Ophthalmol 2009) 3 23
  3. Progression of retinal pigment epithelial alterations during long-term follow-up in female carriers of choroideremia and report of a novel CHM mutation. (PMID: 19597113) Renner A.B. … Kellner U. (Arch. Ophthalmol. 2009) 3 23
  4. CHM gene molecular analysis and X-chromosome inactivation pattern determination in two families with choroideremia. (PMID: 19764077) Perez-Cano H.J. … Zenteno J.C. (Am. J. Med. Genet. A 2009) 3 23
  5. Loss-of-function mutations in Rab escort protein 1 (REP-1) affect intracellular transport in fibroblasts and monocytes of choroideremia patients. (PMID: 20027300) Strunnikova N.V. … Macdonald I.M. (PLoS ONE 2009) 3 23

Products for CHM Gene

Sources for CHM Gene

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