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NM_033109.5(PNPT1):c.2213G>A (p.Arg738His) AND Autosomal recessive nonsyndromic hearing loss 70

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 14, 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:
RCV003448389.2

Allele description [Variation Report for NM_033109.5(PNPT1):c.2213G>A (p.Arg738His)]

NM_033109.5(PNPT1):c.2213G>A (p.Arg738His)

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.2213G>A (p.Arg738His)
HGVS:
  • NC_000002.12:g.55636376C>T
  • NG_033012.1:g.62535G>A
  • NM_033109.5:c.2213G>AMANE SELECT
  • NP_149100.2:p.Arg738His
  • NC_000002.11:g.55863511C>T
  • NM_033109.4:c.2213G>A
Protein change:
R738H
Links:
dbSNP: rs574670461
NCBI 1000 Genomes Browser:
rs574670461
Molecular consequence:
  • NM_033109.5:c.2213G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 70
Synonyms:
Deafness, autosomal recessive 70
Identifiers:
MONDO: MONDO:0013978; MedGen: C1824925; Orphanet: 90636; OMIM: 614934

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004176651Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Feb 14, 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, SCV004176651.1

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

Description

The missense c.2213G>A (p.Arg738His) variant in PNPT1 gene has been submitted to ClinVar as a Variant of Uncertain Significance / Likely pathogenic. The p.Arg738His variant has allele frequency 0.02% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The amino acid change p.Arg738His in PNPT1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 738 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. Functional studies are required to prove the pathogenicity for the variant, for these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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

Last Updated: Jul 15, 2024