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NM_017837.4(PIGV):c.22C>T (p.Arg8Trp) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Nov 26, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001906544.5

Allele description [Variation Report for NM_017837.4(PIGV):c.22C>T (p.Arg8Trp)]

NM_017837.4(PIGV):c.22C>T (p.Arg8Trp)

Gene:
PIGV:phosphatidylinositol glycan anchor biosynthesis class V [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.11
Genomic location:
Preferred name:
NM_017837.4(PIGV):c.22C>T (p.Arg8Trp)
HGVS:
  • NC_000001.11:g.26790837C>T
  • NG_028133.1:g.7875C>T
  • NM_001202554.2:c.22C>T
  • NM_001374478.1:c.22C>T
  • NM_001374480.1:c.22C>T
  • NM_001374481.1:c.22C>T
  • NM_001374482.1:c.22C>T
  • NM_001374483.1:c.-304+3031C>T
  • NM_001374484.1:c.22C>T
  • NM_001374485.1:c.22C>T
  • NM_001374486.1:c.22C>T
  • NM_017837.4:c.22C>TMANE SELECT
  • NP_001189483.1:p.Arg8Trp
  • NP_001361407.1:p.Arg8Trp
  • NP_001361409.1:p.Arg8Trp
  • NP_001361410.1:p.Arg8Trp
  • NP_001361411.1:p.Arg8Trp
  • NP_001361413.1:p.Arg8Trp
  • NP_001361414.1:p.Arg8Trp
  • NP_001361415.1:p.Arg8Trp
  • NP_060307.2:p.Arg8Trp
  • NC_000001.10:g.27117328C>T
  • NM_017837.3:c.22C>T
  • NR_164651.1:n.520C>T
  • NR_164652.1:n.398C>T
Protein change:
R8W
Links:
dbSNP: rs769363441
NCBI 1000 Genomes Browser:
rs769363441
Molecular consequence:
  • NM_001374483.1:c.-304+3031C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001202554.2:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374478.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374480.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374481.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374482.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374484.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374485.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374486.1:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_017837.4:c.22C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164651.1:n.520C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_164652.1:n.398C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002176113Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 11, 2022) 		germlineclinical testing

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

SCV002526556GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Nov 26, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002176113.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 8 of the PIGV protein (p.Arg8Trp). This variant is present in population databases (rs769363441, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PIGV-related conditions. ClinVar contains an entry for this variant (Variation ID: 1402673). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The tryptophan amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV002526556.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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; Has not been previously published as pathogenic or benign to our knowledge

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024