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NM_176787.5(PIGN):c.565G>A (p.Ala189Thr) AND Multiple congenital anomalies-hypotonia-seizures syndrome 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 11, 2021
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:
RCV001886509.6

Allele description [Variation Report for NM_176787.5(PIGN):c.565G>A (p.Ala189Thr)]

NM_176787.5(PIGN):c.565G>A (p.Ala189Thr)

Gene:
PIGN:phosphatidylinositol glycan anchor biosynthesis class N [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.33
Genomic location:
Preferred name:
NM_176787.5(PIGN):c.565G>A (p.Ala189Thr)
HGVS:
  • NC_000018.10:g.62148323C>T
  • NG_033144.1:g.43734G>A
  • NM_012327.6:c.565G>A
  • NM_176787.5:c.565G>AMANE SELECT
  • NP_036459.1:p.Ala189Thr
  • NP_789744.1:p.Ala189Thr
  • NC_000018.9:g.59815556C>T
Protein change:
A189T
Links:
dbSNP: rs2147313473
NCBI 1000 Genomes Browser:
rs2147313473
Molecular consequence:
  • NM_012327.6:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_176787.5:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Multiple congenital anomalies-hypotonia-seizures syndrome 1 (MCAHS1)
Synonyms:
GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 3; PIGN-CDG; Congenital disorder of glycosylation due to PIGN deficiency
Identifiers:
MONDO: MONDO:0013563; MedGen: C3279775; Orphanet: 280633; OMIM: 614080

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002150008Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 11, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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, SCV002150008.3

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

Description

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, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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. This variant has not been reported in the literature in individuals with PIGN-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with threonine at codon 189 of the PIGN protein (p.Ala189Thr). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and threonine.

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

Last Updated: Sep 29, 2024