NM_032634.4(PIGO):c.590C>T (p.Pro197Leu) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 1, 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:: RCV000480492.2

Allele description [Variation Report for NM_032634.4(PIGO):c.590C>T (p.Pro197Leu)]

NM_032634.4(PIGO):c.590C>T (p.Pro197Leu)

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.590C>T (p.Pro197Leu)

HGVS:

NC_000009.12:g.35094281G>A
NG_031990.1:g.7321C>T
NM_001201484.2:c.590C>T
NM_032634.4:c.590C>TMANE SELECT
NM_152850.4:c.590C>T
NP_001188413.1:p.Pro197Leu
NP_116023.2:p.Pro197Leu
NP_690577.2:p.Pro197Leu
NC_000009.11:g.35094278G>A
NM_032634.3:c.590C>T

Protein change:

P197L

Links:

dbSNP: rs150734953

NCBI 1000 Genomes Browser:

rs150734953

Molecular consequence:

NM_001201484.2:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_032634.4:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152850.4:c.590C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000565373	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Nov 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000565373

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Nov 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000565373.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Observed with a pathogenic variant on the opposite allele (in trans) in a patient with features of PIGO-related GPI biosynthesis disorder referred for genetic testing at GeneDx who was also reported in published literature (PMID: 26633542); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26633542)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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