U.S. flag

An official website of the United States government

NM_032634.4(PIGO):c.1114C>T (p.Gln372Ter) AND Hyperphosphatasia with intellectual disability syndrome 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 5, 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:
RCV003074442.3

Allele description [Variation Report for NM_032634.4(PIGO):c.1114C>T (p.Gln372Ter)]

NM_032634.4(PIGO):c.1114C>T (p.Gln372Ter)

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.1114C>T (p.Gln372Ter)
HGVS:
  • NC_000009.12:g.35093035G>A
  • NG_031990.1:g.8567C>T
  • NM_001201484.2:c.1114C>T
  • NM_032634.4:c.1114C>TMANE SELECT
  • NM_152850.4:c.1114C>T
  • NP_001188413.1:p.Gln372Ter
  • NP_116023.2:p.Gln372Ter
  • NP_690577.2:p.Gln372Ter
  • NC_000009.11:g.35093032G>A
Protein change:
Q372*
Molecular consequence:
  • NM_001201484.2:c.1114C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_032634.4:c.1114C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_152850.4:c.1114C>T - nonsense - [Sequence Ontology: SO:0001587]

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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003454590Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 5, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Mutations in PIGO, a member of the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation.

Krawitz PM, Murakami Y, Hecht J, Krüger U, Holder SE, Mortier GR, Delle Chiaie B, De Baere E, Thompson MD, Roscioli T, Kielbasa S, Kinoshita T, Mundlos S, Robinson PN, Horn D.

Am J Hum Genet. 2012 Jul 13;91(1):146-51. doi: 10.1016/j.ajhg.2012.05.004. Epub 2012 Jun 7.

PubMed [citation]
PMID:
22683086
PMCID:
PMC3397269

PIGO mutations in intractable epilepsy and severe developmental delay with mild elevation of alkaline phosphatase levels.

Nakamura K, Osaka H, Murakami Y, Anzai R, Nishiyama K, Kodera H, Nakashima M, Tsurusaki Y, Miyake N, Kinoshita T, Matsumoto N, Saitsu H.

Epilepsia. 2014 Feb;55(2):e13-7. doi: 10.1111/epi.12508. Epub 2014 Jan 13.

PubMed [citation]
PMID:
24417746
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003454590.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is present in population databases (no rsID available, gnomAD 0.003%). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with PIGO-related conditions. This sequence change creates a premature translational stop signal (p.Gln372*) in the PIGO gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PIGO are known to be pathogenic (PMID: 22683086, 24417746).

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

Last Updated: Sep 29, 2024