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NM_033409.4(SLC52A3):c.706G>A (p.Val236Met) AND Brown-Vialetto-van Laere syndrome 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 7, 2023
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:
RCV000810466.6

Allele description

NM_033409.4(SLC52A3):c.706G>A (p.Val236Met)

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.706G>A (p.Val236Met)
HGVS:
  • NC_000020.11:g.763865C>T
  • NG_027687.2:g.17121G>A
  • NM_001370085.1:c.706G>A
  • NM_001370086.1:c.706G>A
  • NM_033409.4:c.706G>AMANE SELECT
  • NP_001357014.1:p.Val236Met
  • NP_001357015.1:p.Val236Met
  • NP_212134.3:p.Val236Met
  • LRG_1394t1:c.706G>A
  • LRG_1394:g.17121G>A
  • LRG_1394p1:p.Val236Met
  • NC_000020.10:g.744509C>T
  • NG_027687.1:g.9720G>A
  • NM_033409.3:c.706G>A
Protein change:
V236M
Links:
dbSNP: rs927297761
NCBI 1000 Genomes Browser:
rs927297761
Molecular consequence:
  • NM_001370085.1:c.706G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370086.1:c.706G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033409.4:c.706G>A - 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
SCV000950667Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 7, 2023) 		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 Invitae, SCV000950667.4

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

Description

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 236 of the SLC52A3 protein (p.Val236Met). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SLC52A3-related conditions. ClinVar contains an entry for this variant (Variation ID: 654493). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SLC52A3 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

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

Last Updated: May 1, 2024