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NM_014251.3(SLC25A13):c.615+5G>A AND Citrin deficiency

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 30, 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:
RCV000811639.7

Allele description

NM_014251.3(SLC25A13):c.615+5G>A

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.615+5G>A
Other names:
IVS6+5G>A
HGVS:
  • NC_000007.14:g.96193032C>T
  • NG_012247.2:g.134116G>A
  • NM_001160210.2:c.615+5G>A
  • NM_014251.3:c.615+5G>AMANE SELECT
  • NC_000007.13:g.95822344C>T
  • NM_014251.2:c.615+5G>A
Links:
dbSNP: rs80338717
NCBI 1000 Genomes Browser:
rs80338717
Molecular consequence:
  • NM_001160210.2:c.615+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_014251.3:c.615+5G>A - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000951915Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 30, 2024) 		germlineclinical testing

PubMed (8)
[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

Citrin deficiency, a perplexing global disorder.

Dimmock D, Maranda B, Dionisi-Vici C, Wang J, Kleppe S, Fiermonte G, Bai R, Hainline B, Hamosh A, O'Brien WE, Scaglia F, Wong LJ.

Mol Genet Metab. 2009 Jan;96(1):44-9. doi: 10.1016/j.ymgme.2008.10.007. Epub 2008 Nov 25.

PubMed [citation]
PMID:
19036621

Citrin Deficiency.

Saheki T, Song YZ.

2005 Sep 16 [updated 2017 Aug 10]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]
PMID:
20301360
See all PubMed Citations (8)

Details of each submission

From Invitae, SCV000951915.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (8)

Description

This sequence change falls in intron 6 of the SLC25A13 gene. It does not directly change the encoded amino acid sequence of the SLC25A13 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs80338717, gnomAD 0.1%). This variant has been observed in individual(s) with citrin deficiency (PMID: 19036621, 20301360, 21134364, 21507300, 24586645; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS6+5G>A. ClinVar contains an entry for this variant (Variation ID: 21517). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in retention of intron 6 and introduces a premature termination codon (PMID: 24586645). The resulting mRNA is expected to undergo nonsense-mediated decay. 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: Jun 23, 2024