NM_006996.3(SLC19A2):c.428C>T (p.Ser143Phe) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 26, 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:: RCV002530823.2

Allele description [Variation Report for NM_006996.3(SLC19A2):c.428C>T (p.Ser143Phe)]

NM_006996.3(SLC19A2):c.428C>T (p.Ser143Phe)

Gene:

SLC19A2:solute carrier family 19 member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q24.2

Genomic location:

Preferred name:

NM_006996.3(SLC19A2):c.428C>T (p.Ser143Phe)

HGVS:

NC_000001.11:g.169477534G>A
NG_008255.1:g.13437C>T
NM_001319667.1:c.205-7348C>T
NM_006996.3:c.428C>TMANE SELECT
NP_008927.1:p.Ser143Phe
NC_000001.10:g.169446772G>A
NM_006996.2:c.428C>T

Protein change:

S143F

Links:

dbSNP: rs761957186

NCBI 1000 Genomes Browser:

rs761957186

Molecular consequence:

NM_001319667.1:c.205-7348C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_006996.3:c.428C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003523352	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 26, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10874303, 29450569, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003523352

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 26, 2022)

germline

clinical testing

PubMed (3)
[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

The spectrum of mutations, including four novel ones, in the thiamine-responsive megaloblastic anemia gene SLC19A2 of eight families.

Raz T, Labay V, Baron D, Szargel R, Anbinder Y, Barrett T, Rabl W, Viana MB, Mandel H, Baruchel A, Cayuela JM, Cohen N.

Hum Mutat. 2000;16(1):37-42.

PubMed [citation]

PMID:: 10874303

Pharmacogenomics in diabetes: outcomes of thiamine therapy in TRMA syndrome.

Habeb AM, Flanagan SE, Zulali MA, Abdullah MA, Pomahačová R, Boyadzhiev V, Colindres LE, Godoy GV, Vasanthi T, Al Saif R, Setoodeh A, Haghighi A, Haghighi A, Shaalan Y; International Neonatal Diabetes Consortium., Hattersley AT, Ellard S, De Franco E.

Diabetologia. 2018 May;61(5):1027-1036. doi: 10.1007/s00125-018-4554-x. Epub 2018 Feb 15.

PubMed [citation]

PMID:: 29450569
PMCID:: PMC6449001

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003523352.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

ClinVar contains an entry for this variant (Variation ID: 492806). For these reasons, this variant has been classified as Pathogenic. 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 expected to disrupt SLC19A2 protein function. This variant is also known as p.S142F. This missense change has been observed in individual(s) with thiamine-responsive megaloblastic anemia (PMID: 10874303, 29450569). This variant is present in population databases (rs761957186, gnomAD 0.006%). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 143 of the SLC19A2 protein (p.Ser143Phe).

#	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 14, 2024

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