NM_014251.3(SLC25A13):c.2T>C (p.Met1Thr) AND Citrullinemia type II

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 27, 2017
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:: RCV001163311.6

Allele description [Variation Report for NM_014251.3(SLC25A13):c.2T>C (p.Met1Thr)]

NM_014251.3(SLC25A13):c.2T>C (p.Met1Thr)

Genes:

LOC129998833:ATAC-STARR-seq lymphoblastoid silent region 18384 [Gene]
SLC25A13:solute carrier family 25 member 13 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.3

Genomic location:

Preferred name:

NM_014251.3(SLC25A13):c.2T>C (p.Met1Thr)

Other names:

p.Met1?

HGVS:

NC_000007.14:g.96321955A>G
NG_012247.2:g.5193T>C
NM_001160210.2:c.2T>C
NM_014251.3:c.2T>CMANE SELECT
NP_001153682.1:p.Met1Thr
NP_055066.1:p.Met1Thr
NC_000007.13:g.95951267A>G
NM_014251.2:c.2T>C
NR_027662.2:n.144T>C

Protein change:

M1T

Links:

dbSNP: rs541276426

NCBI 1000 Genomes Browser:

rs541276426

Molecular consequence:

NM_001160210.2:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_014251.3:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001160210.2:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_014251.3:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_027662.2:n.144T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Citrullinemia type II
Synonyms:: Citrullinemia type 2
Identifiers:: MONDO: MONDO:0016603; MedGen: C1863844

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001325334	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 23022256, 23067347, 23053473 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001325334

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

PubMed (3)
[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

Molecular analysis of SLC25A13 gene in human peripheral blood lymphocytes: Marked transcript diversity, and the feasibility of cDNA cloning as a diagnostic tool for citrin deficiency.

Zhang ZH, Lin WX, Deng M, Zhao XJ, Song YZ.

Gene. 2012 Dec 15;511(2):227-34. doi: 10.1016/j.gene.2012.09.049. Epub 2012 Sep 26.

PubMed [citation]

PMID:: 23022256

Neonatal intrahepatic cholestasis caused by citrin deficiency: prevalence and SLC25A13 mutations among Thai infants.

Treepongkaruna S, Jitraruch S, Kodcharin P, Charoenpipop D, Suwannarat P, Pienvichit P, Kobayashi K, Wattanasirichaigoon D.

BMC Gastroenterol. 2012 Oct 15;12:141. doi: 10.1186/1471-230X-12-141.

PubMed [citation]

PMID:: 23067347
PMCID:: PMC3483206

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001325334.2

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown 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: Jun 17, 2024

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