NM_014251.3(SLC25A13):c.[1956C>A;1962del] AND Neonatal intrahepatic cholestasis due to citrin deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 30, 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:: RCV002508346.5

Alleles description [Variation Report for NM_014251.3(SLC25A13):c.[1956C>A;1962del]]

NM_014251.3(SLC25A13):c.1956C>A (p.Asn652Lys)

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.1956C>A (p.Asn652Lys)

HGVS:

NC_000007.14:g.96121263G>T
NG_012247.2:g.205885C>A
NM_001160210.2:c.1959C>A
NM_014251.3:c.1956C>AMANE SELECT
NP_001153682.1:p.Asn653Lys
NP_055066.1:p.Asn652Lys
NC_000007.13:g.95750575G>T
NM_014251.2:c.1956C>A
NR_027662.2:n.1982C>A

Protein change:

N652K

Links:

dbSNP: rs2485539395

Molecular consequence:

NM_001160210.2:c.1959C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_014251.3:c.1956C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_027662.2:n.1982C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

NM_014251.3(SLC25A13):c.1962del (p.Phe654fs)

Gene:

SLC25A13:solute carrier family 25 member 13 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

7q21.3

Genomic location:

Preferred name:

NM_014251.3(SLC25A13):c.1962del (p.Phe654fs)

HGVS:

NC_000007.14:g.96121259del
NG_012247.2:g.205891del
NM_001160210.2:c.1965del
NM_014251.3:c.1962delMANE SELECT
NP_001153682.1:p.Phe655fs
NP_055066.1:p.Phe654fs
NC_000007.13:g.95750571del
NM_014251.2:c.1962del
NR_027662.2:n.1988del

Protein change:

F654fs

Links:

dbSNP: rs2485539309

Molecular consequence:

NM_001160210.2:c.1965del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014251.3:c.1962del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_027662.2:n.1988del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Neonatal intrahepatic cholestasis due to citrin deficiency (CDNI)
Synonyms:: Neonatal-onset citrullinemia type II; CITRIN DEFICIENCY, NEONATAL OR INFANTILE ONSET; Neonatal-onset citrullinemia type 2
Identifiers:: MONDO: MONDO:0011601; MedGen: C1853942; Orphanet: 247598; OMIM: 605814

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002546526	Genesolutions, Medical Genetics Institutes, Ho Chi Minh City, Vietnam See additional submitters Hepatology Department, National Children’s Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 30, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 36599957, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002546526

Genesolutions, Medical Genetics Institutes, Ho Chi Minh City, Vietnam

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 30, 2022)

germline

clinical testing

PubMed (2)
[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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The mutation spectrum of SLC25A13 gene in citrin deficiency: identification of novel mutations in Vietnamese pediatric cohort with neonatal intrahepatic cholestasis.

Nguyen MT, Nguyen AP, Ngo DN, Nguyen PT, Tang HS, Giang H, Lu YT, Nguyen HN, Tran MD.

J Hum Genet. 2023 May;68(5):305-312. doi: 10.1038/s10038-022-01112-2. Epub 2023 Jan 4.

PubMed [citation]

PMID:: 36599957

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genesolutions, Medical Genetics Institutes, Ho Chi Minh City, Vietnam, SCV002546526.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 16, 2025

ClinVar

Relating variation to medicine