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NM_032634.4(PIGO):c.3261_3262delinsAG (p.Gln1088Glu) AND Hyperphosphatasia with intellectual disability syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 20, 2022
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:
RCV003036371.2

Allele description [Variation Report for NM_032634.4(PIGO):c.3261_3262delinsAG (p.Gln1088Glu)]

NM_032634.4(PIGO):c.3261_3262delinsAG (p.Gln1088Glu)

Gene:
PIGO:phosphatidylinositol glycan anchor biosynthesis class O [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_032634.4(PIGO):c.3261_3262delinsAG (p.Gln1088Glu)
HGVS:
  • NC_000009.12:g.35089100_35089101delinsCT
  • NG_031990.1:g.12501_12502delinsAG
  • NM_001201484.2:c.2010_2011delinsAG
  • NM_032634.4:c.3261_3262delinsAGMANE SELECT
  • NM_152850.4:c.2010_2011delinsAG
  • NP_001188413.1:p.Gln671Glu
  • NP_116023.2:p.Gln1088Glu
  • NP_690577.2:p.Gln671Glu
  • NC_000009.11:g.35089097_35089098delinsCT
Protein change:
Q1088E
Molecular consequence:
  • NM_001201484.2:c.2010_2011delinsAG - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032634.4:c.3261_3262delinsAG - missense variant - [Sequence Ontology: SO:0001583]
  • NM_152850.4:c.2010_2011delinsAG - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hyperphosphatasia with intellectual disability syndrome 2 (HPMRS2)
Synonyms:
GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 6; HYPERPHOSPHATASIA WITH IMPAIRED INTELLECTUAL DEVELOPMENT SYNDROME 2
Identifiers:
MONDO: MONDO:0013882; MedGen: C3553637; Orphanet: 247262; OMIM: 614749

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003347795Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 20, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003347795.1

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

Description

This sequence change replaces glutamine, which is neutral and polar, with glutamic acid, which is acidic and polar, at codon 1088 of the PIGO protein (p.Gln1088Glu). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has not been reported in the literature in individuals affected with PIGO-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024