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NM_014252.4(SLC25A15):c.498del (p.Leu167fs) AND Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Aug 22, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001386805.5

Allele description [Variation Report for NM_014252.4(SLC25A15):c.498del (p.Leu167fs)]

NM_014252.4(SLC25A15):c.498del (p.Leu167fs)

Gene:
SLC25A15:solute carrier family 25 member 15 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q14.11
Genomic location:
Preferred name:
NM_014252.4(SLC25A15):c.498del (p.Leu167fs)
HGVS:
  • NC_000013.11:g.40807339del
  • NG_012248.1:g.22929del
  • NM_014252.4:c.498delMANE SELECT
  • NP_055067.1:p.Leu167fs
  • NC_000013.10:g.41381472del
  • NC_000013.10:g.41381475del
Protein change:
L167fs
Links:
dbSNP: rs2138056689
NCBI 1000 Genomes Browser:
rs2138056689
Molecular consequence:
  • NM_014252.4:c.498del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome (HHHS)
Synonyms:
Ornithine translocase deficiency syndrome; HHH syndrome; Ornithine translocase deficiency
Identifiers:
MONDO: MONDO:0009393; MedGen: C0268540; Orphanet: 415; OMIM: 238970

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001587153Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Apr 5, 2022)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004201680Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Aug 22, 2023)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Clinical and molecular findings in hyperornithinemia-hyperammonemia-homocitrullinuria syndrome.

Salvi S, Santorelli FM, Bertini E, Boldrini R, Meli C, Donati A, Burlina AB, Rizzo C, Di Capua M, Fariello G, Dionisi-Vici C.

Neurology. 2001 Sep 11;57(5):911-4.

PubMed [citation]
PMID:
11552031

Identification of novel mutations in the SLC25A15 gene in hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome: a clinical, molecular, and functional study.

Tessa A, Fiermonte G, Dionisi-Vici C, Paradies E, Baumgartner MR, Chien YH, Loguercio C, de Baulny HO, Nassogne MC, Schiff M, Deodato F, Parenti G, Rutledge SL, Vilaseca MA, Melone MA, Scarano G, Aldamiz-Echevarría L, Besley G, Walter J, Martinez-Hernandez E, Hernandez JM, Pierri CL, et al.

Hum Mutat. 2009 May;30(5):741-8. doi: 10.1002/humu.20930.

PubMed [citation]
PMID:
19242930
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001587153.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1073730). This variant has not been reported in the literature in individuals affected with SLC25A15-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu167Trpfs*27) in the SLC25A15 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A15 are known to be pathogenic (PMID: 11552031, 19242930).

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

From Baylor Genetics, SCV004201680.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024