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NM_030631.4(SLC25A21):c.43C>T (p.Arg15Trp) AND Mitochondrial DNA depletion syndrome 18

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 20, 2023
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:
RCV004771691.1

Allele description [Variation Report for NM_030631.4(SLC25A21):c.43C>T (p.Arg15Trp)]

NM_030631.4(SLC25A21):c.43C>T (p.Arg15Trp)

Genes:
SLC25A21-AS1:SLC25A21 antisense RNA 1 [Gene - HGNC]
SLC25A21:solute carrier family 25 member 21 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q13.3
Genomic location:
Preferred name:
NM_030631.4(SLC25A21):c.43C>T (p.Arg15Trp)
HGVS:
  • NC_000014.9:g.37172308G>A
  • NG_128926.1:g.688G>A
  • NG_128927.1:g.108G>A
  • NM_001171170.2:c.43C>T
  • NM_030631.4:c.43C>TMANE SELECT
  • NP_001164641.1:p.Arg15Trp
  • NP_085134.1:p.Arg15Trp
  • NC_000014.8:g.37641513G>A
  • NR_033240.1:n.283G>A
Protein change:
R15W
Molecular consequence:
  • NM_001171170.2:c.43C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_030631.4:c.43C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_033240.1:n.283G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Mitochondrial DNA depletion syndrome 18
Identifiers:
MONDO: MONDO:0032932; MedGen: C5394140; OMIM: 618811

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV005382373Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(May 20, 2023)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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 Neuberg Centre For Genomic Medicine, NCGM, SCV005382373.1

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

Description

The missense c.43C>T (p.Arg15Trp) variant in the SLC25A21 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is absent in the gnomAD Exomes. The amino acid Arginine at position 15 is changed to a Tryptophan changing protein sequence and it might alter its composition and physico-chemical properties. Multiple lines of computational evidence (Polyphen-Benign, SIFT-Tolerated and MutationTaster-Polymorphism) predict no damaging effect on protein structure and function for this variant. The amino acid Arginine in SLC25A21 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

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

Last Updated: Nov 3, 2024