NM_032634.4(PIGO):c.1673C>T (p.Ala558Val) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 9, 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:
RCV003479296.1

Allele description [Variation Report for NM_032634.4(PIGO):c.1673C>T (p.Ala558Val)]

NM_032634.4(PIGO):c.1673C>T (p.Ala558Val)

Gene:
PIGO:phosphatidylinositol glycan anchor biosynthesis class O [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_032634.4(PIGO):c.1673C>T (p.Ala558Val)
HGVS:
  • NC_000009.12:g.35092214G>A
  • NG_031990.1:g.9388C>T
  • NM_001201484.2:c.1344+329C>T
  • NM_032634.4:c.1673C>TMANE SELECT
  • NM_152850.4:c.1344+329C>T
  • NP_116023.2:p.Ala558Val
  • NC_000009.11:g.35092211G>A
  • NM_032634.3:c.1673C>T
Protein change:
A558V
Links:
dbSNP: rs544432298
NCBI 1000 Genomes Browser:
rs544432298
Molecular consequence:
  • NM_001201484.2:c.1344+329C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_152850.4:c.1344+329C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_032634.4:c.1673C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004223617Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Uncertain significance
(Nov 9, 2023)
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, SCV004223617.1

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

Description

Variant summary: PIGO c.1673C>T (p.Ala558Val) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251368 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.1673C>T in individuals affected with Hyperphosphatasia With Intellectual Disability Syndrome 2 and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited a clinical-significance assessment for this variant to ClinVar after 2014 and has classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Sep 29, 2024