NM_001346754.2(PIGW):c.158G>A (p.Trp53Ter) AND Hyperphosphatasia with intellectual disability syndrome 5

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 11, 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:: RCV003882132.2

Allele description [Variation Report for NM_001346754.2(PIGW):c.158G>A (p.Trp53Ter)]

NM_001346754.2(PIGW):c.158G>A (p.Trp53Ter)

Genes:

MYO19:myosin XIX [Gene - OMIM - HGNC]
PIGW:phosphatidylinositol glycan anchor biosynthesis class W [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_001346754.2(PIGW):c.158G>A (p.Trp53Ter)

HGVS:

NC_000017.11:g.36537259G>A
NG_052004.1:g.7498G>A
NG_052004.2:g.7274G>A
NM_001346754.2:c.158G>AMANE SELECT
NM_001346755.2:c.158G>A
NM_178517.5:c.158G>A
NP_001333683.1:p.Trp53Ter
NP_001333684.1:p.Trp53Ter
NP_848612.2:p.Trp53Ter
NC_000017.10:g.34893108G>A

Protein change:

W53*

Molecular consequence:

NM_001346754.2:c.158G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001346755.2:c.158G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_178517.5:c.158G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Hyperphosphatasia with intellectual disability syndrome 5 (GPIBD11)
Synonyms:: GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 11
Identifiers:: MONDO: MONDO:0014457; MedGen: C4014958; Orphanet: 247262; OMIM: 616025

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004687358	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004687358

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 11, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV004687358.1

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

Description

This sequence change creates a premature translational stop signal (p.Trp53*) in the PIGW gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 452 amino acid(s) of the PIGW protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PIGW-related conditions. 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.

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

Last Updated: Sep 29, 2024

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