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NM_014251.3(SLC25A13):c.1638_1660dup (p.Ala554fs) AND Citrin deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 4, 2024
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:
RCV000822371.9

Allele description [Variation Report for NM_014251.3(SLC25A13):c.1638_1660dup (p.Ala554fs)]

NM_014251.3(SLC25A13):c.1638_1660dup (p.Ala554fs)

Gene:
SLC25A13:solute carrier family 25 member 13 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
7q21.3
Genomic location:
Preferred name:
NM_014251.3(SLC25A13):c.1638_1660dup (p.Ala554fs)
Other names:
1638ins23; p.Ala554Glyfs*17
HGVS:
  • NC_000007.13:g.95751240_95751241insCCCGGGCAGCCACCTGTAATCTC
  • NC_000007.14:g.96121929_96121951dup
  • NG_012247.2:g.205197_205219dup
  • NM_001160210.2:c.1641_1663dup
  • NM_014251.3:c.1638_1660dupMANE SELECT
  • NP_001153682.1:p.Ala555fs
  • NP_055066.1:p.Ala554fs
  • NC_000007.13:g.95751240_95751241insCCCGGGCAGCCACCTGTAATCTC
  • NC_000007.13:g.95751241_95751263dup
  • NC_000007.13:g.95751241_95751263dupCCCGGGCAGCCACCTGTAATCTC
  • NM_014251.2:c.1638_1660dup23
  • NM_014251.3:c.1638_1660dup
  • NR_027662.2:n.1664_1686dup
Protein change:
A554fs
Links:
OMIM: 603859.0003; dbSNP: rs80338725
NCBI 1000 Genomes Browser:
rs80338725
Molecular consequence:
  • NM_001160210.2:c.1641_1663dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_014251.3:c.1638_1660dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_027662.2:n.1664_1686dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000963171Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 4, 2024) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

The gene mutated in adult-onset type II citrullinaemia encodes a putative mitochondrial carrier protein.

Kobayashi K, Sinasac DS, Iijima M, Boright AP, Begum L, Lee JR, Yasuda T, Ikeda S, Hirano R, Terazono H, Crackower MA, Kondo I, Tsui LC, Scherer SW, Saheki T.

Nat Genet. 1999 Jun;22(2):159-63.

PubMed [citation]
PMID:
10369257

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
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000963171.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Ala554Glyfs*17) in the SLC25A13 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A13 are known to be pathogenic (PMID: 10369257, 14680984, 27405544). This variant is present in population databases (rs80338725, gnomAD 0.1%). This premature translational stop signal has been observed in individuals with SLC25A13-related conditions (PMID: 27405544). ClinVar contains an entry for this variant (Variation ID: 6003). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 16, 2025