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Aliases for CHML Gene

Aliases for CHML Gene

  • CHM Like, Rab Escort Protein 2 2 3 5
  • Choroideremia-Like (Rab Escort Protein 2) 2 3
  • Choroideremia-Like Protein 3 4
  • REP2 3 4
  • Rab Proteins Geranylgeranyltransferase Component A 2 3
  • Choroideraemia-Like Protein 3
  • Rab Escort Protein 2 4
  • REP-2 4

External Ids for CHML Gene

Previous GeneCards Identifiers for CHML Gene

  • GC01M239882
  • GC01M237250
  • GC01M238093
  • GC01M238838
  • GC01M238122
  • GC01M239858
  • GC01M241792
  • GC01M212250

Summaries for CHML Gene

Entrez Gene Summary for CHML Gene

  • The product of the CHML gene supports geranylgeranylation of most Rab proteins and may substitute for REP-1 in tissues other than retina. CHML is localized close to the gene for Usher syndrome type II. [provided by RefSeq, Jul 2008]

GeneCards Summary for CHML Gene

CHML (CHM Like, Rab Escort Protein 2) is a Protein Coding gene. Diseases associated with CHML include Choroideremia and Usher Syndrome. Among its related pathways are Metabolism of proteins and RAB GEFs exchange GTP for GDP on RABs. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and Rab geranylgeranyltransferase activity. An important paralog of this gene is CHM.

UniProtKB/Swiss-Prot for CHML Gene

  • Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM in supporting prenylation of Rab3 family.

Gene Wiki entry for CHML Gene

Additional gene information for CHML Gene

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

Genomics for CHML Gene

GeneHancer (GH) Regulatory Elements for CHML Gene

Promoters and enhancers for CHML 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
GH01J241637 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 664.9 +0.3 290 6 HDGF PKNOX1 CLOCK FOXA2 ARNT ARID4B SIN3A ZNF2 YY1 CBX5 CHML OPN3 RPL23AP20 BECN2 RFKP1 GC01M241629
GH01J241603 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 26.1 +31.8 31758 10.5 ATF1 PKNOX1 FOXA2 ARNT ZFP64 SIN3A YBX1 YY1 TCF12 ARID2 KMO CHML WDR64 PLD5 OPN3 GC01M241589 LOC105373233
GH01J241530 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.7 +106.2 106245 6.3 PKNOX1 ATF1 FOXA2 ARNT SIN3A IRF4 YY1 E2F8 ARID2 ATF7 KMO CHML LOC105373233
GH01J241517 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.2 +120.9 120909 2.8 HDGF FOXA2 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 FH LOC105373230 CHML GC01P241514
GH01J241589 Enhancer 1.2 Ensembl ENCODE dbSUPER 16.6 +48.1 48055 5.6 ELF3 MEIS2 JUN BATF BRCA1 RFX5 FOSL1 CTBP1 GATA3 FOSL2 CHML LOC105373233 GC01M241589 KMO OPN3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHML on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHML gene promoter:
  • E47
  • NF-AT3
  • NF-AT2
  • NF-AT1
  • NF-AT
  • NF-AT4
  • CUTL1
  • POU3F1
  • C/EBPalpha
  • AML1a

Genomic Locations for CHML Gene

Genomic Locations for CHML Gene
chr1:241,628,853-241,640,254
(GRCh38/hg38)
Size:
11,402 bases
Orientation:
Minus strand
chr1:241,792,155-241,799,232
(GRCh37/hg19)
Size:
7,078 bases
Orientation:
Minus strand

Genomic View for CHML Gene

Genes around CHML on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CHML Gene

Proteins for CHML Gene

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

    Protein Symbol:
    P26374-RAE2_HUMAN
    Recommended name:
    Rab proteins geranylgeranyltransferase component A 2
    Protein Accession:
    P26374
    Secondary Accessions:
    • B2RAB9
    • Q17RE0
    • Q9H1Y4

    Protein attributes for CHML Gene

    Size:
    656 amino acids
    Molecular mass:
    74071 Da
    Quaternary structure:
    • Monomer. Heterotrimer composed of RABGGTA, RABGGTB and CHML; within this trimer, RABGGTA and RABGGTB form the catalytic component B, while CHML (component A) mediates Rab protein binding. Interacts with RAB1A, RAB7A and RAB27A, but has much lower affinity for RAB1A, RAB7A and RAB27A than CHM.
    Miscellaneous:
    • Substitutes for REP-1 thereby preventing widespread tissue abnormalities in patients with choroideremia who lack REP-1.

neXtProt entry for CHML Gene

Post-translational modifications for CHML Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CHML Gene

Antibody Products

  • Boster Bio Antibodies for CHML
  • Santa Cruz Biotechnology (SCBT) Antibodies for CHML

No data available for DME Specific Peptides for CHML Gene

Domains & Families for CHML Gene

Gene Families for CHML Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for CHML Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P26374

UniProtKB/Swiss-Prot:

RAE2_HUMAN :
  • Belongs to the Rab GDI family.
Family:
  • Belongs to the Rab GDI family.
genes like me logo Genes that share domains with CHML: view

Function for CHML Gene

Molecular function for CHML Gene

UniProtKB/Swiss-Prot Function:
Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM in supporting prenylation of Rab3 family.
GENATLAS Biochemistry:
Rab escort protein-2 activating geranylgeranyltransferase A (prenylating C terminus of RAB (signal transduction)

Phenotypes From GWAS Catalog for CHML Gene

Gene Ontology (GO) - Molecular Function for CHML Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005092 GDP-dissociation inhibitor activity IEA --
GO:0005096 GTPase activator activity IEA --
GO:0017137 Rab GTPase binding IPI 15186776
genes like me logo Genes that share ontologies with CHML: view
genes like me logo Genes that share phenotypes with CHML: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHML

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CHML Gene

Localization for CHML Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHML 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 CHML gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (4)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CHML Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005968 Rab-protein geranylgeranyltransferase complex IEA,IMP 12356470
genes like me logo Genes that share ontologies with CHML: view

Pathways & Interactions for CHML Gene

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

Gene Ontology (GO) - Biological Process for CHML Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0007186 G-protein coupled receptor signaling pathway IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0018344 protein geranylgeranylation IMP,IEA 12356470
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with CHML: view

No data available for SIGNOR curated interactions for CHML Gene

Drugs & Compounds for CHML Gene

No Compound Related Data Available

Transcripts for CHML Gene

mRNA/cDNA for CHML Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(100) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CHML Gene

Choroideremia-like (Rab escort protein 2):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CHML

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

No ASD Table

Relevant External Links for CHML Gene

GeneLoc Exon Structure for
CHML
ECgene alternative splicing isoforms for
CHML

Expression for CHML Gene

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

Protein differential expression in normal tissues from HIPED for CHML Gene

This gene is overexpressed in Fetal Brain (38.8), Frontal cortex (17.6), and Testis (12.6).

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



Protein tissue co-expression partners for CHML Gene

NURSA nuclear receptor signaling pathways regulating expression of CHML Gene:

CHML

SOURCE GeneReport for Unigene cluster for CHML Gene:

Hs.654545

Evidence on tissue expression from TISSUES for CHML Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with CHML: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CHML Gene

Orthologs for CHML Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CHML Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CHML 33
  • 99.39 (n)
dog
(Canis familiaris)
Mammalia CHML 33
  • 88.51 (n)
cow
(Bos Taurus)
Mammalia CHML 34 33
  • 85.9 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Chml 16 34 33
  • 82.88 (n)
rat
(Rattus norvegicus)
Mammalia Chml 33
  • 80.78 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 69 (a)
ManyToMany
-- 34
  • 57 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 62 (a)
ManyToMany
-- 34
  • 57 (a)
ManyToMany
chicken
(Gallus gallus)
Aves CHM 34
  • 66 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 64 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii chm 34 33
  • 58.88 (n)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Rep 34 35
  • 35 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rep-1 34 33
  • 46.71 (n)
OneToMany
Y67D2.1 35
  • 33 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GDI1 34
  • 25 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons REP 33
  • 46.71 (n)
rice
(Oryza sativa)
Liliopsida Os01g0269100 33
  • 45.82 (n)
Species where no ortholog for CHML was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CHML Gene

ENSEMBL:
Gene Tree for CHML (if available)
TreeFam:
Gene Tree for CHML (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CHML: view image

Paralogs for CHML Gene

Paralogs for CHML Gene

(1) SIMAP similar genes for CHML Gene using alignment to 1 proteins:

  • RAE2_HUMAN
genes like me logo Genes that share paralogs with CHML: view

Variants for CHML Gene

Sequence variations from dbSNP and Humsavar for CHML Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000283356 -- 241,636,743(-) G/A upstream_transcript_variant
rs1000467306 -- 241,630,269(-) C/T 3_prime_UTR_variant
rs1000493510 -- 241,632,826(-) G/A 3_prime_UTR_variant
rs1000585332 -- 241,630,010(-) G/C 3_prime_UTR_variant
rs1001239538 -- 241,635,614(-) G/A coding_sequence_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
nsv1002214 CNV gain 25217958
nsv549460 CNV gain 21841781

Variation tolerance for CHML Gene

Residual Variation Intolerance Score: 34.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.76; 47.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHML Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CHML

SNP Genotyping and Copy Number Assay Products

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

Disorders for CHML Gene

MalaCards: The human disease database

(2) MalaCards diseases for CHML Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
choroideremia
  • chm
usher syndrome
  • retinitis pigmentosa-deafness syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CHML in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CHML

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CHML: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CHML Gene

Publications for CHML Gene

  1. Cloning and characterization of the human choroideremia gene. (PMID: 7981670) van Bokhoven H … Cremers FP (Human molecular genetics 1994) 2 3 22 58
  2. REP-2, a Rab escort protein encoded by the choroideremia-like gene. (PMID: 8294464) Cremers FP … Goldstein JL (The Journal of biological chemistry 1994) 3 4 22 58
  3. Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis. (PMID: 19626040) McCauley JL … Haines JL (Genes and immunity 2009) 3 44 58
  4. Identification of a novel asthma susceptibility gene on chromosome 1qter and its functional evaluation. (PMID: 18344558) White JH … Pillai SG (Human molecular genetics 2008) 3 44 58
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58

Products for CHML Gene

Sources for CHML Gene

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