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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 31, 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:: RCV000536292.7

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:: Citrin deficiency
Identifiers:: MONDO: MONDO:0016602; MedGen: C1997910

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000646231	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 31, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25216257, 27405544, 23053473, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000646231

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 31, 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

Inspissated bile syndrome in an infant with citrin deficiency and congenital anomalies of the biliary tract and esophagus: identification and pathogenicity analysis of a novel SLC25A13 mutation with incomplete penetrance.

Zeng HS, Zhao ST, Deng M, Zhang ZH, Cai XR, Chen FP, Song YZ.

Int J Mol Med. 2014 Nov;34(5):1241-8. doi: 10.3892/ijmm.2014.1929. Epub 2014 Sep 10.

PubMed [citation]

PMID:: 25216257
PMCID:: PMC4199400

Molecular diagnosis of pediatric patients with citrin deficiency in China: SLC25A13 mutation spectrum and the geographic distribution.

Lin WX, Zeng HS, Zhang ZH, Mao M, Zheng QQ, Zhao ST, Cheng Y, Chen FP, Wen WR, Song YZ.

Sci Rep. 2016 Jul 11;6:29732. doi: 10.1038/srep29732.

PubMed [citation]

PMID:: 27405544
PMCID:: PMC4942605

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000646231.6

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

Description

This sequence change affects the initiator methionine of the SLC25A13 mRNA. The next in-frame methionine is located at codon 34. This variant is present in population databases (rs541276426, gnomAD 1.2%), including at least one homozygous and/or hemizygous individual. Disruption of the initiator codon has been observed in individual(s) with citrin deficiency (PMID: 25216257, 27405544). ClinVar contains an entry for this variant (Variation ID: 193371). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of the initiator codon affects SLC25A13 function (PMID: 23053473). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain 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: May 12, 2024

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