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NM_000390.4(CHM):c.757C>T (p.Arg253Ter) AND CHM-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 27, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004755834.1

Allele description [Variation Report for NM_000390.4(CHM):c.757C>T (p.Arg253Ter)]

NM_000390.4(CHM):c.757C>T (p.Arg253Ter)

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.757C>T (p.Arg253Ter)
HGVS:
  • NC_000023.11:g.85958923G>A
  • NG_009874.2:g.93640C>T
  • NM_000390.4:c.757C>TMANE SELECT
  • NM_001320959.1:c.313C>T
  • NM_001362517.1:c.313C>T
  • NM_001362518.2:c.313C>T
  • NM_001362519.1:c.313C>T
  • NP_000381.1:p.Arg253Ter
  • NP_001307888.1:p.Arg105Ter
  • NP_001349446.1:p.Arg105Ter
  • NP_001349447.1:p.Arg105Ter
  • NP_001349448.1:p.Arg105Ter
  • LRG_699t1:c.757C>T
  • LRG_699:g.93640C>T
  • NC_000023.10:g.85213928G>A
  • NM_000390.2:c.757C>T
  • NM_000390.3:c.757C>T
Protein change:
R105*
Links:
dbSNP: rs886041178
NCBI 1000 Genomes Browser:
rs886041178
Molecular consequence:
  • NM_000390.4:c.757C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001320959.1:c.313C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001362517.1:c.313C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001362518.2:c.313C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001362519.1:c.313C>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
SCV005360341PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Sep 27, 2024) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV005360341.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CHM c.757C>T variant is predicted to result in premature protein termination (p.Arg253*). This variant has been reported as causative for choroideremia (see for examples van den Hurk et al. 2003. PubMed ID: 12827496; MacDonald et al. 2009. PubMed ID: 19422966; Hayakawa et al. 1999. PubMed ID: 10420196). This variant has not been reported in a large population database, indicating this variant is rare. Nonsense variants in CHM are expected to be pathogenic, and this variant has been classified as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/279774). Given all the evidence, we interpret c.757C>T (p.Arg253*) as pathogenic.

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

Last Updated: Dec 28, 2024