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CHM Gene(Protein Coding)

CHM, Rab Escort Protein 1

GCID:
GC0XM085861
GIFtS:
47
Genes Participants
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Aliases for CHM Gene

Aliases for CHM Gene

  • CHM, Rab Escort Protein 1 2 3 5
  • Choroideremia (Rab Escort Protein 1) 2 3
  • REP-1 3 4
  • TCD 3 4
  • Rab Proteins Geranylgeranyltransferase Component A 1 3
  • 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 Choroid Disease. Among its related pathways are Gene Expression and Metabolism of proteins. Gene Ontology (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

Additional gene information for CHM Gene

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

Genomics for CHM Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for CHM Gene

Promoters and enhancers for CHM Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XJ086046 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.4 362 2.4 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B E2F8 ZNF143 DEK SP3 CHM ENSG00000199567
GH0XJ086001 Enhancer 0.9 Ensembl ENCODE 20 +45.1 45073 1 SOX13 KLF1 FOXA2 SAP130 NFRKB ARID4B KAT7 ZNF614 FOXK2 PRDM10 CHM PIR43538 GC0XM085907
GH0XJ086023 Enhancer 0.3 FANTOM5 17.1 +23.6 23630 0.4 CHM ENSG00000199567
GH0XJ085992 Enhancer 0.7 ENCODE 6.6 +54.1 54053 1.9 MEIS2 JUN FEZF1 KLF14 FOSL1 FOS KLF8 ZNF639 GFI1B CBFA2T3 CHM PIR43538 GC0XM085907
GH0XJ085996 Enhancer 0.3 ENCODE 12.5 +50.8 50810 0.2 NANOG CHM PIR43538 GC0XM085907
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CHM on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for CHM Gene

Genomic Locations for CHM Gene
chrX:85,861,180-86,047,562
(GRCh38/hg38)
Size:
186,383 bases
Orientation:
Minus strand
chrX:85,116,185-85,302,566
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for CHM Gene

Proteins for CHM Gene

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  2. Protein
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  • 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

Protein Expression for CHM Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CHM Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CHM Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CHM Gene

Domains & Families for CHM Gene

Gene Families for CHM Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CHM Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CHM Gene

GenScript: Design optimal peptide antigens:

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

Function for CHM Gene

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  2. CRISPR
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  4. Inhibitory RNA
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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.

Phenotypes From GWAS Catalog for CHM Gene

Gene Ontology (GO) - Molecular Function for CHM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004663 Rab geranylgeranyltransferase activity TAS 8380507
GO:0005092 GDP-dissociation inhibitor activity IEA --
GO:0005096 GTPase activator activity IEA --
GO:0017137 Rab GTPase binding IPI 7957092
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:
  • Chm Chm<tm1Jvdh>
  • Chm Chm<tm1.2Seab>
  • Chm Chm<tm1.3Seab>

Animal Model Products

miRNA for CHM Gene

miRTarBase miRNAs that target CHM

Clone Products

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CHM gene
Compartment Confidence
cytosol 5
nucleus 3
endoplasmic reticulum 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CHM Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005968 Rab-protein geranylgeranyltransferase complex TAS,IDA 7957092
genes like me logo Genes that share ontologies with CHM: view

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:0006886 intracellular protein transport IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0007601 visual perception TAS,IEA --
GO:0018344 protein geranylgeranylation IDA,TAS 7957092
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

Products:

  1. Drug

(1) Drugs for CHM Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CHM Gene

(104) Selected AceView cDNA sequences:
(15) Additional mRNA sequences :
(13) REFSEQ mRNAs :
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CHM Gene

Choroideremia (Rab escort protein 1):
Representative Sequences:

Clone Products

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

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CHM Gene

mRNA expression in normal human tissues for CHM Gene
mRNA expression by GTEx for CHM GenemRNA expression by BioGPS 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, MaxQB, and MOPED for CHM Gene



Protein tissue co-expression partners for CHM Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CHM Gene:

CHM

SOURCE GeneReport for Unigene cluster for CHM Gene:

Hs.496449

Evidence on tissue expression from TISSUES for CHM Gene

  • Nervous system(4.7)
  • Eye(4.5)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CHM Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns with CHM: view

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
chimpanzee
(Pan troglodytes)
 Mammalia CHM 34 33
  • 99.74 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia CHM 34 33
  • 90.64 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia CHM 34 33
  • 90.3 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Chm 33
  • 86.4 (n)
mouse
(Mus musculus)
 Mammalia Chm 16 34 33
  • 86.3 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 34
  • 71 (a)
 ManyToMany
-- 34
  • 58 (a)
 ManyToMany
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 63 (a)
 ManyToMany
-- 34
  • 54 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves CHM 34 33
  • 69.98 (n)
 OneToMany
lizard
(Anolis carolinensis)
 Reptilia -- 34
  • 64 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia chml 33
  • 63.88 (n)
African clawed frog
(Xenopus laevis)
 Amphibia MGC68578 33
zebrafish
(Danio rerio)
 Actinopterygii chm 34
  • 53 (a)
 OneToMany
Dr.17040 33
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.635 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP010419 33
  • 51.07 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Rep 34 35 33
  • 46.41 (n)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea rep-1 34
  • 34 (a)
 OneToMany
Y67D2.1 35
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes GDI1 34
  • 24 (a)
 OneToMany
Species where no ortholog for CHM was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for CHM: view image

Paralogs for CHM Gene

Paralogs for CHM Gene

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

  • RAE1_HUMAN
  • B4DRL9_HUMAN
  • Q8N917_HUMAN
genes like me logo Genes that share paralogs with CHM: view

Variants for CHM Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for CHM Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1057516265 likely-pathogenic, Choroideremia 86,047,532(-) T/C 5_prime_UTR_variant, genic_upstream_transcript_variant, initiator_codon_variant, missense_variant, upstream_transcript_variant
rs132630263 pathogenic, Choroideremia 85,900,700(-) GG/TC coding_sequence_variant, genic_downstream_transcript_variant, stop_gained
rs132630264 pathogenic, Choroideremia 85,894,214(-) G/T coding_sequence_variant, genic_downstream_transcript_variant, stop_gained
rs132630265 pathogenic, Choroideremia 85,894,227(-) C/A coding_sequence_variant, genic_downstream_transcript_variant, stop_gained
rs132630266 pathogenic, Choroideremia, not provided 85,957,918(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, stop_gained

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

Variant ID Type Subtype PubMed ID
dgv2326e212 CNV gain 25503493
dgv2327e212 CNV gain 25503493
dgv2328e212 CNV loss 25503493
esv2740276 CNV deletion 23290073
esv2740277 CNV deletion 23290073
esv3574139 CNV loss 25503493
esv3574140 CNV loss 25503493
esv3574145 CNV loss 25503493
esv3576956 CNV gain 25503493
esv3576967 CNV gain 25503493
nsv438141 CNV loss 16468122
nsv510545 OTHER sequence alteration 20534489
nsv519786 CNV gain 19592680

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)

Additional Variant Information for CHM Gene

Human Gene Mutation Database (HGMD)
CHM
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHM

SNP Genotyping and Copy Number Assay Products

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

Disorders for CHM Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
choroideremia
  • chm
choroid disease
  • abnormality of the choroid
x-linked disease
acute closed-angle glaucoma
  • acute angle-closure glaucoma
dyscalculia
  • disorder of arithmetical skills
- 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

Additional Disease Information for CHM

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 YV … Macdonald IM (Mutation research 2009) 3 4 22 58
  2. Rab escort protein-1 is a multifunctional protein that accompanies newly prenylated rab proteins to their target membranes. (PMID: 7957092) Alexandrov K … Zerial M (The EMBO journal 1994) 3 4 22 58
  3. Comprehensive mutation analysis (20 families) of the choroideremia gene reveals a missense variant that prevents the binding of REP1 with Rab geranylgeranyl transferase. (PMID: 21905166) Esposito G … Salvatore F (Human mutation 2011) 3 4 58
  4. Loss-of-function mutations in Rab escort protein 1 (REP-1) affect intracellular transport in fibroblasts and monocytes of choroideremia patients. (PMID: 20027300) Strunnikova NV … Macdonald IM (PloS one 2009) 3 22 58
  5. CHM gene molecular analysis and X-chromosome inactivation pattern determination in two families with choroideremia. (PMID: 19764077) Perez-Cano HJ … Zenteno JC (American journal of medical genetics. Part A 2009) 3 22 58

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Sources for CHM Gene

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