NM_033409.4(SLC52A3):c.134C>T (p.Thr45Met) AND Brown-Vialetto-van Laere syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 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:: RCV000653711.5

Allele description [Variation Report for NM_033409.4(SLC52A3):c.134C>T (p.Thr45Met)]

NM_033409.4(SLC52A3):c.134C>T (p.Thr45Met)

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.134C>T (p.Thr45Met)

HGVS:

NC_000020.11:g.765641G>A
NG_027687.2:g.15345C>T
NM_001370085.1:c.134C>T
NM_001370086.1:c.134C>T
NM_033409.4:c.134C>TMANE SELECT
NP_001357014.1:p.Thr45Met
NP_001357015.1:p.Thr45Met
NP_212134.3:p.Thr45Met
LRG_1394t1:c.134C>T
LRG_1394:g.15345C>T
LRG_1394p1:p.Thr45Met
NC_000020.10:g.746285G>A
NG_027687.1:g.7944C>T
NM_033409.3:c.134C>T

Protein change:

T45M

Links:

dbSNP: rs776065357

NCBI 1000 Genomes Browser:

rs776065357

Molecular consequence:

NM_001370085.1:c.134C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370086.1:c.134C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033409.4:c.134C>T - 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
SCV000775597	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 28, 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

SCV000775597

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 28, 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000775597.3

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

Description

This sequence change replaces threonine with methionine at codon 45 of the SLC52A3 protein (p.Thr45Met). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs776065357, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with SLC52A3-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

#	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: Feb 7, 2023

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