NM_014251.3(SLC25A13):c.1895C>T (p.Pro632Leu) AND Citrin deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 30, 2021
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:: RCV002961979.2

Allele description [Variation Report for NM_014251.3(SLC25A13):c.1895C>T (p.Pro632Leu)]

NM_014251.3(SLC25A13):c.1895C>T (p.Pro632Leu)

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.1895C>T (p.Pro632Leu)

HGVS:

NC_000007.14:g.96121324G>A
NG_012247.2:g.205824C>T
NM_001160210.2:c.1898C>T
NM_014251.3:c.1895C>TMANE SELECT
NP_001153682.1:p.Pro633Leu
NP_055066.1:p.Pro632Leu
NC_000007.13:g.95750636G>A
NR_027662.2:n.1921C>T

Protein change:

P632L

Molecular consequence:

NM_001160210.2:c.1898C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_014251.3:c.1895C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_027662.2:n.1921C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

Recent activity

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Ribonuclease H [Caenorhabditis elegans]
Ribonuclease H [Caenorhabditis elegans]
gi|392891918|ref|NP_496526.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003279628	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 30, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 14680984, 18392553, 23053473, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003279628

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 30, 2021)

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

Screening of nine SLC25A13 mutations: their frequency in patients with citrin deficiency and high carrier rates in Asian populations.

Kobayashi K, Bang Lu Y, Xian Li M, Nishi I, Hsiao KJ, Choeh K, Yang Y, Hwu WL, Reichardt JK, Palmieri F, Okano Y, Saheki T.

Mol Genet Metab. 2003 Nov;80(3):356-9.

PubMed [citation]

PMID:: 14680984

Identification of 13 novel mutations including a retrotransposal insertion in SLC25A13 gene and frequency of 30 mutations found in patients with citrin deficiency.

Tabata A, Sheng JS, Ushikai M, Song YZ, Gao HZ, Lu YB, Okumura F, Iijima M, Mutoh K, Kishida S, Saheki T, Kobayashi K.

J Hum Genet. 2008;53(6):534-545. doi: 10.1007/s10038-008-0282-2. Epub 2008 Apr 5.

PubMed [citation]

PMID:: 18392553

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003279628.1

#	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 replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 632 of the SLC25A13 protein (p.Pro632Leu). This variant is present in population databases (rs573420716, gnomAD 0.02%). This missense change has been observed in individual(s) with citrin deficiency (PMID: 14680984, 18392553). 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 not expected to disrupt SLC25A13 protein function. Experimental studies have shown that this missense change does not substantially affect 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: Sep 29, 2024

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