NM_033409.4(SLC52A3):c.3G>A (p.Met1Ile) AND Brown-Vialetto-van Laere syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 17, 2021
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:: RCV001932045.6

Allele description [Variation Report for NM_033409.4(SLC52A3):c.3G>A (p.Met1Ile)]

NM_033409.4(SLC52A3):c.3G>A (p.Met1Ile)

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.3G>A (p.Met1Ile)

HGVS:

NC_000020.11:g.765772C>T
NG_027687.2:g.15214G>A
NM_001370085.1:c.3G>A
NM_001370086.1:c.3G>A
NM_033409.4:c.3G>AMANE SELECT
NP_001357014.1:p.Met1Ile
NP_001357015.1:p.Met1Ile
NP_212134.3:p.Met1Ile
LRG_1394t1:c.3G>A
LRG_1394:g.15214G>A
LRG_1394p1:p.Met1Ile
NC_000020.10:g.746416C>T

Protein change:

M1I

Links:

dbSNP: rs2122527408

NCBI 1000 Genomes Browser:

rs2122527408

Molecular consequence:

NM_001370085.1:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001370086.1:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_033409.4:c.3G>A - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001370085.1:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370086.1:c.3G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_033409.4:c.3G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002123867	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 17, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002123867

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 17, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

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, SCV002123867.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals with SLC52A3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change affects the initiator methionine of the SLC52A3 mRNA. The next in-frame methionine is located at codon 5.

#	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: Sep 29, 2024

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