NM_001346754.2(PIGW):c.5C>A (p.Ser2Tyr) AND Hyperphosphatasia with intellectual disability syndrome 5

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 3, 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:: RCV003748589.2

Allele description [Variation Report for NM_001346754.2(PIGW):c.5C>A (p.Ser2Tyr)]

NM_001346754.2(PIGW):c.5C>A (p.Ser2Tyr)

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.5C>A (p.Ser2Tyr)

HGVS:

NC_000017.11:g.36537106C>A
NG_052004.1:g.7345C>A
NG_052004.2:g.7121C>A
NM_001346754.2:c.5C>AMANE SELECT
NM_001346755.2:c.5C>A
NM_178517.5:c.5C>A
NP_001333683.1:p.Ser2Tyr
NP_001333684.1:p.Ser2Tyr
NP_848612.2:p.Ser2Tyr
NC_000017.10:g.34892955C>A

Protein change:

S2Y

Molecular consequence:

NM_001346754.2:c.5C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001346755.2:c.5C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_178517.5:c.5C>A - 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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cysteine and histidine-rich domain-containing protein 1 isoform b [Homo sapiens]
cysteine and histidine-rich domain-containing protein 1 isoform b [Homo sapiens]
gi|221316570|ref|NP_001137545.1|

Protein
non-ribosomal peptide synthetase, partial [Streptomyces rubicolor]
non-ribosomal peptide synthetase, partial [Streptomyces rubicolor]
gi|238770568|dbj|BAH68650.1|

Protein
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Radiogrammitis subpinnatifida ribosomal protein S4 (rps4) gene, partial cds; rps...
Radiogrammitis subpinnatifida ribosomal protein S4 (rps4) gene, partial cds; rps4-trnS intergenic spacer, complete sequence; and tRNA-Ser gene, partial sequence; chloroplast
gi|2082544864|gb|MT648253.1|

Nucleotide
Radiogrammitis ligulata voucher K.R. Wood 11047 (PTBG) ribulose-1,5-bisphosphate...
Radiogrammitis ligulata voucher K.R. Wood 11047 (PTBG) ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast
gi|2070985875|gb|MT657606.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004379164	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 3, 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

SCV004379164

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 3, 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, SCV004379164.1

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

Description

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. 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. This variant has not been reported in the literature in individuals affected with PIGW-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 2 of the PIGW protein (p.Ser2Tyr).

#	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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