NM_001363118.2(SLC52A2):c.383C>T (p.Ser128Leu) AND Inborn genetic diseases

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 17, 2020
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:: RCV001266471.3

Allele description [Variation Report for NM_001363118.2(SLC52A2):c.383C>T (p.Ser128Leu)]

NM_001363118.2(SLC52A2):c.383C>T (p.Ser128Leu)

Gene:

SLC52A2:solute carrier family 52 member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q24.3

Genomic location:

Preferred name:

NM_001363118.2(SLC52A2):c.383C>T (p.Ser128Leu)

HGVS:

NC_000008.11:g.144359875C>T
NG_032872.2:g.6319C>T
NM_001253815.2:c.383C>T
NM_001253816.2:c.383C>T
NM_001363118.2:c.383C>TMANE SELECT
NM_001363120.2:c.383C>T
NM_001363121.2:c.383C>T
NM_001363122.2:c.131-240C>T
NM_024531.5:c.383C>T
NP_001240744.1:p.Ser128Leu
NP_001240745.1:p.Ser128Leu
NP_001350047.1:p.Ser128Leu
NP_001350049.1:p.Ser128Leu
NP_001350050.1:p.Ser128Leu
NP_078807.1:p.Ser128Leu
NC_000008.10:g.145583535C>T
NG_032872.1:g.6319C>T
NM_024531.3:c.383C>T
NM_024531.4:c.383C>T
NR_045600.2:n.843C>T

Protein change:

S128L

Links:

dbSNP: rs374071862

NCBI 1000 Genomes Browser:

rs374071862

Molecular consequence:

NM_001363122.2:c.131-240C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001253815.2:c.383C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001253816.2:c.383C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363118.2:c.383C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363120.2:c.383C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001363121.2:c.383C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024531.5:c.383C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_045600.2:n.843C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001444646	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Jan 17, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25356970, 29053833 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001444646

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Jan 17, 2020)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions.

Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Tippin Davis B, Baxter RM, Zeng W, Mroske C, Parra MC, Gandomi SK, Lu I, Li X, Lu H, Lu HM, Salvador D, Ruble D, Lao M, Fischbach S, Wen J, Lee S, Elliott A, et al.

Genet Med. 2015 Jul;17(7):578-86. doi: 10.1038/gim.2014.154. Epub 2014 Nov 13.

PubMed [citation]

PMID:: 25356970

Clinical, pathological and functional characterization of riboflavin-responsive neuropathy.

Manole A, Jaunmuktane Z, Hargreaves I, Ludtmann MHR, Salpietro V, Bello OD, Pope S, Pandraud A, Horga A, Scalco RS, Li A, Ashokkumar B, Lourenço CM, Heales S, Horvath R, Chinnery PF, Toro C, Singleton AB, Jacques TS, Abramov AY, Muntoni F, Hanna MG, et al.

Brain. 2017 Nov 1;140(11):2820-2837. doi: 10.1093/brain/awx231.

PubMed [citation]

PMID:: 29053833
PMCID:: PMC5808726

Details of each submission

From Ambry Genetics, SCV001444646.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The p.S128L pathogenic mutation (also known as c.383C>T), located in coding exon 2 of the SLC52A2 gene, results from a C to T substitution at nucleotide position 383. The serine at codon 128 is replaced by leucine, an amino acid with dissimilar properties. This alteration has been reported in two patients with Brown-Vialetto-Van Laere (BVVL) syndrome and confirmed to be in trans with another pathogenic mutation in an affected patient (Farwell KD et al. Genet. Med., 2015 Jul;17:578-86; Manole A et al. Brain, 2017 11;140:2820-2837). This variant is rare in population-based cohorts with an overall frequency of approximately 0.002% (6/282600) in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

#	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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