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NM_033409.4(SLC52A3):c.796C>T (p.Arg266Trp) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 2, 2018
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:
RCV000483942.2

Allele description [Variation Report for NM_033409.4(SLC52A3):c.796C>T (p.Arg266Trp)]

NM_033409.4(SLC52A3):c.796C>T (p.Arg266Trp)

Gene:
SLC52A3:solute carrier family 52 member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20p13
Genomic location:
Preferred name:
NM_033409.4(SLC52A3):c.796C>T (p.Arg266Trp)
HGVS:
  • NC_000020.11:g.763775G>A
  • NG_027687.2:g.17211C>T
  • NM_001370085.1:c.796C>T
  • NM_001370086.1:c.796C>T
  • NM_033409.4:c.796C>TMANE SELECT
  • NP_001357014.1:p.Arg266Trp
  • NP_001357015.1:p.Arg266Trp
  • NP_212134.3:p.Arg266Trp
  • LRG_1394t1:c.796C>T
  • LRG_1394:g.17211C>T
  • LRG_1394p1:p.Arg266Trp
  • NC_000020.10:g.744419G>A
  • NG_027687.1:g.9810C>T
  • NM_033409.3:c.796C>T
  • Q9NQ40:p.Arg266Trp
Protein change:
R266W; Arg266Trp
Links:
UniProtKB: Q9NQ40#VAR_077428; dbSNP: rs370499474
NCBI 1000 Genomes Browser:
rs370499474
Molecular consequence:
  • NM_001370085.1:c.796C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370086.1:c.796C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033409.4:c.796C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000567641GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jul 2, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000567641.4

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

Description

The R266W variant in the SLC52A3 gene has been reported previously in association with autosomal recessive Brown-Vialetto-Van Laere syndrome 1 (Ciccolella et al., 2012). has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is observed in 5/126660 (0.0039%) alleles from individuals of non-Finnish European background in large population cohorts, with no homozygotes identified (Lek et al., 2016). The R266W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function.We interpret R266W as a variant of uncertain significance.

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

Last Updated: May 1, 2024