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NM_181882.3(PRX):c.2775_2776insT (p.Lys926Ter) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 28, 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:
RCV001008051.1

Allele description [Variation Report for NM_181882.3(PRX):c.2775_2776insT (p.Lys926Ter)]

NM_181882.3(PRX):c.2775_2776insT (p.Lys926Ter)

Gene:
PRX:periaxin [Gene - OMIM - HGNC]
Variant type:
Insertion
Cytogenetic location:
19q13.2
Genomic location:
Preferred name:
NM_181882.3(PRX):c.2775_2776insT (p.Lys926Ter)
HGVS:
  • NC_000019.10:g.40395576_40395577insA
  • NG_007979.1:g.22788_22789insT
  • NM_020956.2:c.*2980_*2981insT
  • NM_181882.3:c.2775_2776insTMANE SELECT
  • NP_870998.2:p.Lys926Ter
  • LRG_265t1:c.*2980_*2981insT
  • LRG_265t2:c.2775_2776insT
  • LRG_265:g.22788_22789insT
  • NC_000019.9:g.40901483_40901484insA
  • NM_181882.2:c.2775_2776insT
Protein change:
K926*
Links:
dbSNP: rs1599652316
NCBI 1000 Genomes Browser:
rs1599652316
Molecular consequence:
  • NM_020956.2:c.*2980_*2981insT - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_181882.3:c.2775_2776insT - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001167784GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Nov 28, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV001167784.1

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

Description

A variant that is likely pathogenic has been identified in the PRX gene. The c.2775_2776insT variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.2775_2776insT variant in the PRX gene causes a frameshift starting with codon Lysine 926, and changes this amino acid to a Stop codon residue, denoted p.Lys926Ter. This nonsense variant in the C-terminus is predicted to result in protein truncation, as the last 536 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014). The c.2775_2776insT variant is not observed in large population cohorts (Lek et al., 2016). Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Apr 23, 2022