NM_004278.4(PIGL):c.493A>C (p.Arg165=) AND not provided

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

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 11, 2022
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:: RCV002515973.3

Allele description

NM_004278.4(PIGL):c.493A>C (p.Arg165=)

Gene:

PIGL:phosphatidylinositol glycan anchor biosynthesis class L [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p11.2

Genomic location:

Preferred name:

NM_004278.4(PIGL):c.493A>C (p.Arg165=)

HGVS:

NC_000017.11:g.16313613A>C
NG_032651.1:g.101419A>C
NM_004278.4:c.493A>CMANE SELECT
NP_004269.1:p.Arg165=
NC_000017.10:g.16216927A>C
NM_004278.3:c.493A>C

Links:

dbSNP: rs184077858

NCBI 1000 Genomes Browser:

rs184077858

Molecular consequence:

NM_004278.4:c.493A>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens neutrophil cytosolic factor 2 (NCF2), transcript variant...
PREDICTED: Homo sapiens neutrophil cytosolic factor 2 (NCF2), transcript variant X4, mRNA
gi|2462509510|ref|XM_054336754.1|

Nucleotide
PREDICTED: Homo sapiens neutrophil cytosolic factor 2 (NCF2), transcript variant...
PREDICTED: Homo sapiens neutrophil cytosolic factor 2 (NCF2), transcript variant X6, mRNA
gi|2462509514|ref|XM_054336756.1|

Nucleotide
PREDICTED: Homo sapiens T cell immune regulator 1, ATPase H+ transporting V0 sub...
PREDICTED: Homo sapiens T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 (TCIRG1), transcript variant X4, mRNA
gi|2462522463|ref|XM_054367445.1|

Nucleotide
Sphingobacterium sp. HMSC13C05
Sphingobacterium sp. HMSC13C05
HMP reference genome

BioProject
V-type proton ATPase 116 kDa subunit a 3 isoform X2 [Homo sapiens]
V-type proton ATPase 116 kDa subunit a 3 isoform X2 [Homo sapiens]
gi|2217280781|ref|XP_047282195.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003296323	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 11, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005192748	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003296323

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 11, 2022)

germline

clinical testing

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

SCV005192748

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

germline

not provided

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	yes	not provided	not provided	not provided	not provided	not provided	not provided
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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Invitae, SCV003296323.2

#	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 sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 159710). This variant has not been reported in the literature in individuals affected with PIGL-related conditions. This variant is present in population databases (rs184077858, gnomAD 0.04%). This sequence change affects codon 165 of the PIGL mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PIGL protein. It affects a nucleotide within the consensus splice site.

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005192748.1

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

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

Last Updated: Sep 16, 2024

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