NM_001346754.2(PIGW):c.106dup (p.Arg36fs) AND Hyperphosphatasia with intellectual disability syndrome 5

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 13, 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:: RCV003049861.3

Allele description [Variation Report for NM_001346754.2(PIGW):c.106dup (p.Arg36fs)]

NM_001346754.2(PIGW):c.106dup (p.Arg36fs)

Genes:

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

Variant type:

Duplication

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_001346754.2(PIGW):c.106dup (p.Arg36fs)

HGVS:

NC_000017.11:g.36537207dup
NG_052004.1:g.7446dup
NG_052004.2:g.7222dup
NM_001346754.2:c.106dupMANE SELECT
NM_001346755.2:c.106dup
NM_178517.5:c.106dup
NP_001333683.1:p.Arg36fs
NP_001333684.1:p.Arg36fs
NP_848612.2:p.Arg36fs
NC_000017.10:g.34893055_34893056insA
NC_000017.10:g.34893056dup

Protein change:

R36fs

Molecular consequence:

NM_001346754.2:c.106dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001346755.2:c.106dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_178517.5:c.106dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003344116	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 13, 2022)	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

SCV003344116

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 13, 2022)

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, SCV003344116.2

#	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.Arg36Lysfs*21) in the PIGW gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 469 amino acid(s) of the PIGW protein. This variant is present in population databases (rs759234429, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PIGW-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.

#	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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