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NM_007254.4(PNKP):c.610C>T (p.Arg204Ter) AND not specified

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 20, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_007254.4(PNKP):c.610C>T (p.Arg204Ter)]

NM_007254.4(PNKP):c.610C>T (p.Arg204Ter)

PNKP:polynucleotide kinase 3'-phosphatase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_007254.4(PNKP):c.610C>T (p.Arg204Ter)
Other names:
  • NC_000019.10:g.49864205G>A
  • NG_027717.1:g.8361C>T
  • NM_007254.4:c.610C>TMANE SELECT
  • NP_009185.2:p.Arg204Ter
  • NC_000019.9:g.50367462G>A
  • NM_007254.2:c.610C>T
  • NM_007254.3:c.610C>T
Protein change:
dbSNP: rs796052850
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_007254.4:c.610C>T - nonsense - [Sequence Ontology: SO:0001587]


MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001339109Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Mar 20, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001339109.1

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


Variant summary: PNKP c.610C>T (p.Arg204X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been reported as disease-associated mutations in HGMD and in the literature and have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 4e-06 in 251368 control chromosomes (gnomAD). To our knowledge, no occurrence of c.610C>T in individuals affected with PNKP-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submitter (evaluation in 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Apr 23, 2022