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NM_033409.4(SLC52A3):c.1062C>G (p.Phe354Leu) AND Brown-Vialetto-van Laere syndrome 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 26, 2022
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:
RCV001365658.7

Allele description [Variation Report for NM_033409.4(SLC52A3):c.1062C>G (p.Phe354Leu)]

NM_033409.4(SLC52A3):c.1062C>G (p.Phe354Leu)

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.1062C>G (p.Phe354Leu)
HGVS:
  • NC_000020.11:g.763509G>C
  • NG_027687.2:g.17477C>G
  • NM_001370085.1:c.1062C>G
  • NM_001370086.1:c.1062C>G
  • NM_033409.4:c.1062C>GMANE SELECT
  • NP_001357014.1:p.Phe354Leu
  • NP_001357015.1:p.Phe354Leu
  • NP_212134.3:p.Phe354Leu
  • LRG_1394t1:c.1062C>G
  • LRG_1394:g.17477C>G
  • LRG_1394p1:p.Phe354Leu
  • NC_000020.10:g.744153G>C
Protein change:
F354L
Links:
dbSNP: rs2122515947
NCBI 1000 Genomes Browser:
rs2122515947
Molecular consequence:
  • NM_001370085.1:c.1062C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370086.1:c.1062C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033409.4:c.1062C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Brown-Vialetto-van Laere syndrome 1
Synonyms:
BULBAR PALSY, PROGRESSIVE, WITH SENSORINEURAL DEAFNESS; PONTOBULBAR PALSY WITH DEAFNESS; Pontobulbar palsy and neurosensory deafness; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0024537; MedGen: C0796274; Orphanet: 97229; OMIM: 211530

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001561934Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 26, 2022) 		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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001561934.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1056779). This variant has not been reported in the literature in individuals affected with SLC52A3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 354 of the SLC52A3 protein (p.Phe354Leu).

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

Last Updated: Sep 29, 2024