NM_001346754.2(PIGW):c.776A>G (p.Asn259Ser) AND Hyperphosphatasia with intellectual disability syndrome 5

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 8, 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:: RCV002596126.1

Allele description

NM_001346754.2(PIGW):c.776A>G (p.Asn259Ser)

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.776A>G (p.Asn259Ser)

HGVS:

NC_000017.11:g.36537877A>G
NG_052004.2:g.7892A>G
NM_001346754.2:c.776A>GMANE SELECT
NM_001346755.2:c.776A>G
NM_178517.3:c.776A>G
NM_178517.5:c.776A>G
NP_001333683.1:p.Asn259Ser
NP_001333684.1:p.Asn259Ser
NP_848612.2:p.Asn259Ser
NC_000017.10:g.34893726A>G
NG_052004.1:g.8116A>G

Protein change:

N259S

Molecular consequence:

NM_001346754.2:c.776A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346755.2:c.776A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_178517.5:c.776A>G - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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Saccharomyces cerevisiae S288C U2-type spliceosomal complex subunit CWC22 (CWC22...
Saccharomyces cerevisiae S288C U2-type spliceosomal complex subunit CWC22 (CWC22), partial mRNA
gi|398366394|ref|NM_001181407.3|

Nucleotide
ZK632.4 putative mannose-6-phosphate isomerase [Caenorhabditis elegans]
ZK632.4 putative mannose-6-phosphate isomerase [Caenorhabditis elegans]
Gene ID:176388

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003502940	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 8, 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

SCV003502940

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 8, 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 Invitae, SCV003502940.1

#	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 replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 259 of the PIGW protein (p.Asn259Ser). This variant is present in population databases (rs768798408, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PIGW-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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: May 1, 2024

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