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NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter) AND SLC24A1-related disorder

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 26, 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:
RCV004754746.1

Allele description [Variation Report for NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter)]

NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter)

Gene:
SLC24A1:solute carrier family 24 member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q22.31
Genomic location:
Preferred name:
NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter)
HGVS:
  • NC_000015.10:g.65639613C>T
  • NG_031968.2:g.33209C>T
  • NM_001301031.1:c.1963C>T
  • NM_001301032.1:c.1909C>T
  • NM_001301033.2:c.1909C>T
  • NM_004727.3:c.1963C>TMANE SELECT
  • NP_001287960.1:p.Arg655Ter
  • NP_001287961.1:p.Arg637Ter
  • NP_001287962.1:p.Arg637Ter
  • NP_004718.1:p.Arg655Ter
  • NC_000015.9:g.65931951C>T
  • NM_004727.2:c.1963C>T
Protein change:
R637*
Links:
dbSNP: rs201452975
NCBI 1000 Genomes Browser:
rs201452975
Molecular consequence:
  • NM_001301031.1:c.1963C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001301032.1:c.1909C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001301033.2:c.1909C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004727.3:c.1963C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
SLC24A1-related disorder
Synonyms:
SLC24A1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005346949PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely pathogenic
(Mar 26, 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, SCV005346949.1

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

Description

The SLC24A1 c.1963C>T variant is predicted to result in premature protein termination (p.Arg655*). This variant was reported in the homozygous state in an individual with congenital stationary night blindness (Martin-Merida et al 2019. PubMed ID: 30902645). This variant is reported in 0.053% of alleles in individuals of Latino descent in gnomAD. Nonsense variants in SLC24A1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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

Last Updated: Oct 13, 2024