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NM_015937.6(PIGT):c.1342C>T (p.Arg448Trp)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Jun 1, 2021
Accession:
VCV000143194.3
Variation ID:
143194
Description:
single nucleotide variant
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NM_015937.6(PIGT):c.1342C>T (p.Arg448Trp)

Allele ID
152912
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
20q13.12
Genomic location
20: 45424323 (GRCh38) GRCh38 UCSC
20: 44052963 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000020.11:g.45424323C>T
NC_000020.10:g.44052963C>T
NM_015937.6:c.1342C>T MANE Select NP_057021.2:p.Arg448Trp missense
... more HGVS
Protein change
R448W, R346W, R381W, R392W
Other names
R488W
Canonical SPDI
NC_000020.11:45424322:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00002
Links
ClinGen: CA170098
OMIM: 610272.0004
dbSNP: rs527236031
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, single submitter Dec 31, 2018 RCV000132728.3
Pathogenic 1 criteria provided, single submitter Jun 1, 2021 RCV001531960.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PIGT - - GRCh38
GRCh37
94 104

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Dec 31, 2018)
criteria provided, single submitter
Method: clinical testing
Multiple congenital anomalies-hypotonia-seizures syndrome 3
Allele origin: germline
Invitae
Accession: SCV000957008.1
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces arginine with tryptophan at codon 448 of the PIGT protein (p.Arg448Trp). The arginine residue is moderately conserved and there is a … (more)
Pathogenic
(Jun 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001747312.1
Submitted: (Jul 04, 2021)
Evidence details
pathogenic
(-)
no assertion criteria provided
Method: not provided
Multiple congenital anomalies-hypotonia-seizures syndrome 3
Allele origin: inherited
Undiagnosed Diseases Program Translational Research Laboratory,National Institutes of Health
Accession: SCV000187657.1
Submitted: (Aug 05, 2014)
Evidence details
Comment:
Converted during submission to Pathogenic.
Pathogenic
(Apr 25, 2016)
no assertion criteria provided
Method: literature only
MULTIPLE CONGENITAL ANOMALIES-HYPOTONIA-SEIZURES SYNDROME 3
Allele origin: germline
OMIM
Accession: SCV000267597.1
Submitted: (Apr 25, 2016)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Expanding the clinical and molecular characteristics of PIGT-CDG, a disorder of glycosylphosphatidylinositol anchors. Lam C Molecular genetics and metabolism 2015 PMID: 25943031
Novel compound heterozygous PIGT mutations caused multiple congenital anomalies-hypotonia-seizures syndrome 3. Nakashima M Neurogenetics 2014 PMID: 24906948

Text-mined citations for rs527236031...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jul 13, 2021