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NM_033109.5(PNPT1):c.1619A>G (p.Asn540Ser) AND Combined oxidative phosphorylation defect type 13

Germline classification:
Uncertain significance (1 submission)
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:
RCV003339565.2

Allele description [Variation Report for NM_033109.5(PNPT1):c.1619A>G (p.Asn540Ser)]

NM_033109.5(PNPT1):c.1619A>G (p.Asn540Ser)

Gene:
PNPT1:polyribonucleotide nucleotidyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p16.1
Genomic location:
Preferred name:
NM_033109.5(PNPT1):c.1619A>G (p.Asn540Ser)
HGVS:
  • NC_000002.12:g.55646470T>C
  • NG_033012.1:g.52441A>G
  • NM_033109.5:c.1619A>GMANE SELECT
  • NP_149100.2:p.Asn540Ser
  • NC_000002.11:g.55873605T>C
  • NC_000002.11:g.55873605T>C
  • NM_033109.4:c.1619A>G
  • p.N540S
Protein change:
N540S
Links:
dbSNP: rs202190573
NCBI 1000 Genomes Browser:
rs202190573
Molecular consequence:
  • NM_033109.5:c.1619A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Combined oxidative phosphorylation defect type 13
Synonyms:
Combined oxidative phosphorylation deficiency 13
Identifiers:
MONDO: MONDO:0013977; MedGen: C4706283; Orphanet: 319514; OMIM: 614932

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004048004Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significancegermlineclinical 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, SCV004048004.1

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

Description

The missense variant c.1619A>G (p.Asn540Ser) in PNPT1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has been reported to the ClinVar database as Pathogenic. The p.Asn540Ser variant is reported with allele frequency of 0.02% in gnomAD exomes and novel in gnomAD Exomes and 1000 Genomes. The amino acid Asn at position 540 is changed to a Ser changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Asn540Ser in PNPT1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. In the absence of another reportable variant the molecular diagnosis is not confirmed.

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

Last Updated: Apr 6, 2024