NM_004727.3(SLC24A1):c.1963C>T (p.Arg655Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 21, 2024
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:: RCV001380449.5

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001578530	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 21, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20850105, 26822852, 30902645, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001578530

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 21, 2024)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A mutation in SLC24A1 implicated in autosomal-recessive congenital stationary night blindness.

Riazuddin SA, Shahzadi A, Zeitz C, Ahmed ZM, Ayyagari R, Chavali VR, Ponferrada VG, Audo I, Michiels C, Lancelot ME, Nasir IA, Zafar AU, Khan SN, Husnain T, Jiao X, MacDonald IM, Riazuddin S, Sieving PA, Katsanis N, Hejtmancik JF.

Am J Hum Genet. 2010 Oct 8;87(4):523-31. doi: 10.1016/j.ajhg.2010.08.013. Epub 2010 Sep 16.

PubMed [citation]

PMID:: 20850105
PMCID:: PMC2948789

Next-generation sequencing confirms the implication of SLC24A1 in autosomal-recessive congenital stationary night blindness.

Neuillé M, Malaichamy S, Vadalà M, Michiels C, Condroyer C, Sachidanandam R, Srilekha S, Arokiasamy T, Letexier M, Démontant V, Sahel JA, Sen P, Audo I, Soumittra N, Zeitz C.

Clin Genet. 2016 Jun;89(6):690-9. doi: 10.1111/cge.12746. Epub 2016 Mar 4.

PubMed [citation]

PMID:: 26822852

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001578530.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Arg655*) in the SLC24A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC24A1 are known to be pathogenic (PMID: 20850105, 26822852). This variant is present in population databases (rs201452975, gnomAD 0.06%). This premature translational stop signal has been observed in individual(s) with night blindness (PMID: 30902645). ClinVar contains an entry for this variant (Variation ID: 1068778). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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