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NM_000390.4(CHM):c.130G>T (p.Gly44Ter) AND CHM-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 12, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003909900.1

Allele description

NM_000390.4(CHM):c.130G>T (p.Gly44Ter)

Gene:
CHM:CHM Rab escort protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq21.2
Genomic location:
Preferred name:
NM_000390.4(CHM):c.130G>T (p.Gly44Ter)
HGVS:
  • NC_000023.11:g.85981796C>A
  • NG_009874.2:g.70767G>T
  • NM_000390.3:c.130G>T
  • NM_000390.4:c.130G>TMANE SELECT
  • NM_001145414.4:c.130G>T
  • NM_001320959.1:c.-315G>T
  • NM_001362517.1:c.-315G>T
  • NM_001362518.2:c.-311G>T
  • NM_001362519.1:c.-311G>T
  • NP_000381.1:p.Gly44Ter
  • NP_001138886.1:p.Gly44Ter
  • LRG_699t1:c.130G>T
  • LRG_699:g.70767G>T
  • NC_000023.10:g.85236800C>A
  • NM_000390.2:c.130G>T
Protein change:
G44*
Links:
dbSNP: rs886041175
NCBI 1000 Genomes Browser:
rs886041175
Molecular consequence:
  • NM_001320959.1:c.-315G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001362517.1:c.-315G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001362518.2:c.-311G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001362519.1:c.-311G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000390.4:c.130G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001145414.4:c.130G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
CHM-related disorder
Synonyms:
CHM-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004722748PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Dec 12, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004722748.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The CHM c.130G>T variant is predicted to result in premature protein termination (p.Gly44*). This variant has been reported in individuals with choroideremia (McTaggart et al. 2002. PubMed ID: 12203991; Table S1 in Xue et al. 2018. PubMed ID: 30297895; Table S4 in Panneman et al. 2023. PubMed ID: 36819107). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in CHM are expected to be pathogenic. Given the evidence, we interpret this variant as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024