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NM_032634.4(PIGO):c.626A>G (p.Asn209Ser) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 16, 2024
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:
RCV004586694.1

Allele description [Variation Report for NM_032634.4(PIGO):c.626A>G (p.Asn209Ser)]

NM_032634.4(PIGO):c.626A>G (p.Asn209Ser)

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.626A>G (p.Asn209Ser)
HGVS:
  • NC_000009.12:g.35094245T>C
  • NG_031990.1:g.7357A>G
  • NM_001201484.2:c.626A>G
  • NM_032634.4:c.626A>GMANE SELECT
  • NM_152850.4:c.626A>G
  • NP_001188413.1:p.Asn209Ser
  • NP_116023.2:p.Asn209Ser
  • NP_690577.2:p.Asn209Ser
  • NC_000009.11:g.35094242T>C
  • NM_032634.3:c.626A>G
Protein change:
N209S
Links:
dbSNP: rs138028827
NCBI 1000 Genomes Browser:
rs138028827
Molecular consequence:
  • NM_001201484.2:c.626A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032634.4:c.626A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152850.4:c.626A>G - 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
SCV005076118Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Uncertain significance
(Apr 16, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Summary from all submissions

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

Citations

PubMed

High frequency of heterozygous rare variants of the SLC34A1 and SLC9A3R1 genes in patients with atypical femur fracture.

Marini F, Giusti F, Marasco E, Xumerle L, Kwiatkowska KM, Garagnani P, Biver E, Ferrari S, Iolascon G, Iantomasi T, Brandi ML.

Eur J Endocrinol. 2023 Jan 10;188(1). doi:pii: lvad001. 10.1093/ejendo/lvad001.

PubMed [citation]
PMID:
36762943

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005076118.1

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

Description

Variant summary: PIGO c.626A>G (p.Asn209Ser) results in a conservative amino acid change located in the GPI ethanolamine phosphate transferase 3, N-terminal domain (IPR037675) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0008 in 238830 control chromosomes. c.626A>G has been reported in the literature in an individual affected with atypical femur fracture (e.g. Marini_2023). This report do not provide unequivocal conclusions about association of the variant with Hyperphosphatasia With Intellectual Disability Syndrome 2. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 36762943). ClinVar contains an entry for this variant (Variation ID: 366761). 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: Oct 8, 2024