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NM_014252.4(SLC25A15):c.147C>G (p.Asp49Glu) AND Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 31, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000877375.15

Allele description [Variation Report for NM_014252.4(SLC25A15):c.147C>G (p.Asp49Glu)]

NM_014252.4(SLC25A15):c.147C>G (p.Asp49Glu)

Gene:
SLC25A15:solute carrier family 25 member 15 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q14.11
Genomic location:
Preferred name:
NM_014252.4(SLC25A15):c.147C>G (p.Asp49Glu)
HGVS:
  • NC_000013.11:g.40799148C>G
  • NG_012248.1:g.14738C>G
  • NM_014252.4:c.147C>GMANE SELECT
  • NP_055067.1:p.Asp49Glu
  • NC_000013.10:g.41373284C>G
  • NM_014252.3:c.147C>G
  • NR_038258.1:n.2199G>C
  • NR_038259.1:n.2028G>C
Protein change:
D49E
Links:
dbSNP: rs187685447
NCBI 1000 Genomes Browser:
rs187685447
Molecular consequence:
  • NM_014252.4:c.147C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_038258.1:n.2199G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_038259.1:n.2028G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV001020105Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 31, 2024)
germlineclinical testing

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

SCV001269009Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Uncertain significance
(Jan 12, 2018)
germlineclinical testing

Citation Link,

SCV001454137Natera, Inc.
no assertion criteria provided
Uncertain significance
(Apr 16, 2020)
germlineclinical testing

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001020105.6

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

From Illumina Laboratory Services, Illumina, SCV001269009.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

From Natera, Inc., SCV001454137.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024