NM_025243.4(SLC19A3):c.1112C>T (p.Ala371Val) AND Biotin-responsive basal ganglia disease

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Jan 24, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000624942.10

Allele description [Variation Report for NM_025243.4(SLC19A3):c.1112C>T (p.Ala371Val)]

NM_025243.4(SLC19A3):c.1112C>T (p.Ala371Val)

Gene:

SLC19A3:solute carrier family 19 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q36.3

Genomic location:

Preferred name:

NM_025243.4(SLC19A3):c.1112C>T (p.Ala371Val)

HGVS:

NC_000002.12:g.227695949G>A
NG_016359.1:g.27081C>T
NM_025243.4:c.1112C>TMANE SELECT
NP_079519.1:p.Ala371Val
NC_000002.11:g.228560665G>A
NM_025243.3:c.1112C>T

Protein change:

A371V

Links:

dbSNP: rs142166552

NCBI 1000 Genomes Browser:

rs142166552

Molecular consequence:

NM_025243.4:c.1112C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Biotin-responsive basal ganglia disease (BBTGD)
Synonyms:: Biotin-thiamine-responsive basal ganglia disease; Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2); Thiamine metabolism dysfunction syndrome type 2; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011841; MedGen: C1843807; Orphanet: 199348; OMIM: 607483

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000743150	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Jul 28, 2017)	germline	clinical testing	Citation Link,
SCV000744176	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Dec 10, 2015)	germline	clinical testing	Citation Link,
SCV000824873	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 24, 2024)	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

SCV000743150

Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely benign
(Jul 28, 2017)

germline

clinical testing

Citation Link,

SCV000744176

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely benign
(Dec 10, 2015)

germline

clinical testing

Citation Link,

SCV000824873

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 24, 2024)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743150.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000744176.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV000824873.6

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

#	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: Mar 5, 2024

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