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NM_015937.6(PIGT):c.417C>T (p.Cys139=) AND Multiple congenital anomalies-hypotonia-seizures syndrome 3

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 4, 2023
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:
RCV001408861.6

Allele description

NM_015937.6(PIGT):c.417C>T (p.Cys139=)

Gene:
PIGT:phosphatidylinositol glycan anchor biosynthesis class T [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q13.12
Genomic location:
Preferred name:
NM_015937.6(PIGT):c.417C>T (p.Cys139=)
HGVS:
  • NC_000020.11:g.45418903C>T
  • NG_047154.1:g.7837C>T
  • NM_001184728.3:c.326-392C>T
  • NM_001184729.3:c.417C>T
  • NM_001184730.3:c.188-392C>T
  • NM_015937.6:c.417C>TMANE SELECT
  • NP_001171658.1:p.Cys139=
  • NP_057021.2:p.Cys139=
  • NC_000020.10:g.44047543C>T
  • NR_047691.2:n.393C>T
  • NR_047693.2:n.433C>T
  • NR_047694.2:n.255C>T
Links:
dbSNP: rs150090118
NCBI 1000 Genomes Browser:
rs150090118
Molecular consequence:
  • NM_001184728.3:c.326-392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001184730.3:c.188-392C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NR_047691.2:n.393C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_047693.2:n.433C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_047694.2:n.255C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001184729.3:c.417C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_015937.6:c.417C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Multiple congenital anomalies-hypotonia-seizures syndrome 3 (MCAHS3)
Synonyms:
GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 7
Identifiers:
MONDO: MONDO:0014165; MedGen: C3809356; Orphanet: 369837; OMIM: 615398

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001610871Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Aug 4, 2023) 		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 Invitae, SCV001610871.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024