NM_033409.4(SLC52A3):c.51G>A (p.Trp17Ter) AND Brown-Vialetto-van Laere syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 29, 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:: RCV003599066.1

Allele description [Variation Report for NM_033409.4(SLC52A3):c.51G>A (p.Trp17Ter)]

NM_033409.4(SLC52A3):c.51G>A (p.Trp17Ter)

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.51G>A (p.Trp17Ter)

HGVS:

NC_000020.11:g.765724C>T
NG_027687.2:g.15262G>A
NM_001370085.1:c.51G>A
NM_001370086.1:c.51G>A
NM_033409.4:c.51G>AMANE SELECT
NP_001357014.1:p.Trp17Ter
NP_001357015.1:p.Trp17Ter
NP_212134.3:p.Trp17Ter
LRG_1394t1:c.51G>A
LRG_1394:g.15262G>A
LRG_1394p1:p.Trp17Ter
NC_000020.10:g.746368C>T

Protein change:

W17*

Molecular consequence:

NM_001370085.1:c.51G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001370086.1:c.51G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_033409.4:c.51G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004414161	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 29, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20206331, 22824638, 25462087, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004414161

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 29, 2022)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Brown-Vialetto-Van Laere syndrome, a ponto-bulbar palsy with deafness, is caused by mutations in c20orf54.

Green P, Wiseman M, Crow YJ, Houlden H, Riphagen S, Lin JP, Raymond FL, Childs AM, Sheridan E, Edwards S, Josifova DJ.

Am J Hum Genet. 2010 Mar 12;86(3):485-9. doi: 10.1016/j.ajhg.2010.02.006. Epub 2010 Mar 4.

PubMed [citation]

PMID:: 20206331
PMCID:: PMC2833371

Brown-Vialetto-van Laere and Fazio-Londe overlap syndromes: a clinical, biochemical and genetic study.

Ciccolella M, Catteruccia M, Benedetti S, Moroni I, Uziel G, Pantaleoni C, Chiapparini L, Bizzi A, D'Amico A, Fattori F, Salsano ML, Pastore A, Tozzi G, Piemonte F, Bertini E.

Neuromuscul Disord. 2012 Dec;22(12):1075-82. doi: 10.1016/j.nmd.2012.05.007. Epub 2012 Jul 21.

PubMed [citation]

PMID:: 22824638

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004414161.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. 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 creates a premature translational stop signal (p.Trp17*) in the SLC52A3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC52A3 are known to be pathogenic (PMID: 20206331, 22824638, 25462087).

#	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 28, 2024

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