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NM_007254.4(PNKP):c.1497G>A (p.Leu499=) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Dec 1, 2018
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:
RCV002311642.9

Allele description [Variation Report for NM_007254.4(PNKP):c.1497G>A (p.Leu499=)]

NM_007254.4(PNKP):c.1497G>A (p.Leu499=)

Gene:
PNKP:polynucleotide kinase 3'-phosphatase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.33
Genomic location:
Preferred name:
NM_007254.4(PNKP):c.1497G>A (p.Leu499=)
Other names:
p.L499L:CTG>CTA
HGVS:
  • NC_000019.10:g.49861317C>T
  • NG_027717.1:g.11249G>A
  • NG_050666.1:g.17474C>T
  • NM_007254.4:c.1497G>AMANE SELECT
  • NP_009185.2:p.Leu499=
  • NC_000019.9:g.50364574C>T
  • NM_007254.2:c.1497G>A
  • NM_007254.3:c.1497G>A
  • NP_009185.2:p.(=)
Links:
dbSNP: rs142199280
NCBI 1000 Genomes Browser:
rs142199280
Molecular consequence:
  • NM_007254.4:c.1497G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000847248Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Dec 1, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000847248.5

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Nov 3, 2024