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

Summary

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

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of REP1 impacts choroidal melanogenesis and vasculogenesis in choroideremia.
Title: Loss of REP1 impacts choroidal melanogenesis and vasculogenesis in choroideremia.
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.
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.
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.
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.
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.
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.
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.
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.
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	not available

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 CatalogPubMed EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CHM (e-PCR)
- UniSTS:498196

GDB:636299 (e-PCR)
- UniSTS:99386

WI-11849 (e-PCR)
- UniSTS:10308

GDB:636308 (e-PCR)
- UniSTS:158532

GDB:636311 (e-PCR)
- UniSTS:158533

GDB:636322 (e-PCR)
- UniSTS:158534

GDB:636328 (e-PCR)
- UniSTS:158535

GDB:437724 (e-PCR)
- UniSTS:157256

GDB:636338 (e-PCR)
- UniSTS:158536

GDB:636342 (e-PCR)
- UniSTS:158537

STS-M83773 (e-PCR)
- UniSTS:27467

GDB:636348 (e-PCR)
- UniSTS:158539

CHM_8255 (e-PCR)
- UniSTS:468331

RH46170 (e-PCR)
- UniSTS:54429

GDB:636379 (e-PCR)
- UniSTS:99010

L29953 (e-PCR)
- UniSTS:52164

GDB:271316 (e-PCR)
- UniSTS:156357

GDB:271320 (e-PCR)
- UniSTS:156358

PMC22091P1 (e-PCR)
- UniSTS:272093

RH80031 (e-PCR)
- UniSTS:91103

GDB:452659 (e-PCR)
- UniSTS:157407

DXS8326 (e-PCR)
- UniSTS:80096

RH119297 (e-PCR)
- UniSTS:133859

RH112 (e-PCR)
- UniSTS:38396

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

NG_009874.2 RefSeqGene

Range

5001..191383

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_699

mRNA and Protein(s)

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
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
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
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
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
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

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

85861180..86047558 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DRL9
XM_047441794.1 → XP_047297750.1 rab proteins geranylgeranyltransferase component A 1 isoform X2

UniProtKB/TrEMBL

B4DRL9
XM_017029242.3 → XP_016884731.1 rab proteins geranylgeranyltransferase component A 1 isoform X1

UniProtKB/TrEMBL

A8K545

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

84292297..84478778 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DRL9
XM_054326409.1 → XP_054182384.1 rab proteins geranylgeranyltransferase component A 1 isoform X2

UniProtKB/TrEMBL

B4DRL9
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

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.
NM_152579.2: Suppressed sequence

Description

NM_152579.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.