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NM_032634.4(PIGO):c.1681T>A (p.Phe561Ile) AND Hyperphosphatasia with intellectual disability syndrome 2

Germline classification:
Uncertain significance (1 submission)
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:
RCV003444426.2

Allele description [Variation Report for NM_032634.4(PIGO):c.1681T>A (p.Phe561Ile)]

NM_032634.4(PIGO):c.1681T>A (p.Phe561Ile)

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.1681T>A (p.Phe561Ile)
HGVS:
  • NC_000009.12:g.35092206A>T
  • NG_031990.1:g.9396T>A
  • NM_001201484.2:c.1344+337T>A
  • NM_032634.4:c.1681T>AMANE SELECT
  • NM_152850.4:c.1344+337T>A
  • NP_116023.2:p.Phe561Ile
  • NC_000009.11:g.35092203A>T
Protein change:
F561I
Molecular consequence:
  • NM_001201484.2:c.1344+337T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_152850.4:c.1344+337T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_032634.4:c.1681T>A - 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
SCV004171359Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004171359.1

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

Description

The missense c.1681T>A(p.Phe561Ile) variant in PIGO gene has not been reported previously as a pathogenic variant nor a benign variant, to our knowledge. The p.Phe561Ile variant is novel (not in any individuals) in both gnomAD Exomes and 1000 Genomes databases. This variant has not been reported to the ClinVar database. The amino acid change p.Phe561Ile in PIGO is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Phe at position 561 is changed to a Ile changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance (VUS).

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

Last Updated: Apr 6, 2024