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NM_002641.4(PIGA):c.986T>C (p.Val329Ala) AND Multiple congenital anomalies-hypotonia-seizures syndrome 2

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 2, 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:
RCV001775167.1

Allele description [Variation Report for NM_002641.4(PIGA):c.986T>C (p.Val329Ala)]

NM_002641.4(PIGA):c.986T>C (p.Val329Ala)

Gene:
PIGA:phosphatidylinositol glycan anchor biosynthesis class A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.2
Genomic location:
Preferred name:
NM_002641.4(PIGA):c.986T>C (p.Val329Ala)
HGVS:
  • NC_000023.11:g.15324867A>G
  • NG_009786.1:g.15672T>C
  • NM_002641.4:c.986T>CMANE SELECT
  • NM_020473.3:c.284T>C
  • NP_002632.1:p.Val329Ala
  • NP_065206.3:p.Val95Ala
  • LRG_160t1:c.986T>C
  • LRG_160:g.15672T>C
  • NC_000023.10:g.15342989A>G
  • NM_002641.3:c.986T>C
  • NR_033835.1:n.728T>C
  • NR_033836.1:n.444T>C
Protein change:
V329A
Links:
dbSNP: rs1921924356
NCBI 1000 Genomes Browser:
rs1921924356
Molecular consequence:
  • NM_002641.4:c.986T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_020473.3:c.284T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_033835.1:n.728T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_033836.1:n.444T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2)
Synonyms:
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 20; GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 4
Identifiers:
MONDO: MONDO:0010466; MedGen: C3275508; Orphanet: 300496; OMIM: 300868

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0020123343billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Oct 2, 2021) 		maternalclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedmaternalyes1not providednot provided1not providedclinical testing

Citations

PubMed

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 3billion, SCV002012334.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

It is not observed in the gnomAD v2.1.1 dataset (PM2). Missense changes are a common disease-causing mechanism (PP2). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.937, 3Cnet: 0.991, PP3). Patient's phenotype is considered compatible with Multiple congenital anomalies-hypotonia-seizures syndrome 2 (3billion dataset, PP4).Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyes1not providednot provided1not providednot providednot provided

Last Updated: Oct 8, 2024