NM_005609.3(PYGM):c.148C>T (p.Arg50Ter)

Variation ID: Help
2298
Review status: Help
criteria provided, multiple submitters, no conflicts2 stars out of maximum of 4 stars

Interpretation Help

Clinical significance:
Pathogenic
Last evaluated:
Sep 21, 2016
Number of submission(s):
8
Condition(s):
See supporting ClinVar records

Allele(s) Help

NM_005609.3(PYGM):c.148C>T (p.Arg50Ter)

Allele ID:
17337
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.1
Genomic location:
  • Chr11: 64759751 (on Assembly GRCh38)
  • Chr11: 64527223 (on Assembly GRCh37)
Other names:
  • Arg49*
  • MA R49x
  • R49X
Protein change:
R50*
HGVS:
  • NG_013018.1:g.5965C>T
  • NM_005609.3:c.148C>T
  • NP_005600.1:p.Arg50Ter
  • NC_000011.10:g.64759751G>A (GRCh38)
  • NC_000011.9:g.64527223G>A (GRCh37)
  • NM_005609.2:c.148C>T
  • NP_005600.1:p.Arg50*
Links:
NCBI 1000 Genomes Browser:
rs116987552
Molecular consequence:
NM_005609.3:c.148C>T: nonsense [Sequence Ontology SO:0001587]
Allele frequency:
  • GO-ESP 0.00223 (A)
  • GMAF 0.00100 (A)
  • ExAC 0.00137 (A)

1 Affected gene

Variant frequency in dbGaP Help

NM_005609.3(PYGM):c.148C>T (p.Arg50Ter)

GRCh37 Chr11:64527223
Called variantsPotential variants
Sample count30 of 8506152 of 40998

Called variants are samples submitted to dbGaP that have the variant allele. Potential variants are SRA runs that display the allele in at least 30% of the reads covering the position, and have 10 or more passing reads covering the position.

Browser views

Assertion and evidence details

Germline

Clinical significance
(Last evaluated)
Review status
(Assertion method)
Collection methodCondition(s)
(Mode of inheritance)
OriginCitationsSubmitter - Study nameSubmission accession
Pathogenic
(Sep 21, 2016)
criteria provided, single submitter
clinical testinggermline
    GeneDxSCV000329478.3
    Pathogenic
    (Jun 14, 2016)
    criteria provided, single submitter
    clinical testinggermlineIllumina Clinical Services Laboratory,IlluminaSCV000373042.2
    Pathogenic
    (Mar 8, 2016)
    criteria provided, single submitter
    clinical testingunknown
      CounsylSCV000485127.1
      Pathogenic
      (Jul 6, 2016)
      criteria provided, single submitter
      clinical testinggermline
        Center for Pediatric Genomic Medicine,Children's Mercy Hospital and ClinicsSCV000511631.1
        Pathogenic
        (Dec 19, 2014)
        criteria provided, single submitter
        clinical testinggermline
          Emory Genetics Laboratory,Emory UniversitySCV000077245.2
          Pathogenic
          (Aug 10, 2012)
          no assertion criteria providedclinical testinggermlineEmory Genetics Laboratory,Emory UniversitySCV000113224.3
          Pathogenic
          (Jun 26, 2014)
          no assertion criteria providedliterature onlygermlineGeneReviewsSCV000172194.2
          Pathogenic
          (Jul 1, 2007)
          no assertion criteria providedliterature onlygermlineOMIMSCV000022546.4
          SubmitterFamiliesIndividualsAllele originEthnicityGeographic originCitations and DatabasesDescription
          Total for all submittersnot provided46germline, unknownnot providednot provided
          Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinicsnot providednot providedgermlinenot providednot providednot providednot provided
          Counsylnot providednot providedunknownnot providednot providednot providednot provided
          Emory Genetics Laboratory,Emory Universitynot provided46germlinenot providednot providednot providednot provided
          GeneDxnot providednot providedgermlinenot providednot providednot providedA published pathogenic variant…Full description
          GeneReviewsnot providednot providedgermlinenot providednot providednot provided
          Illumina Clinical Services Laboratory,Illuminanot providednot providedgermlinenot providednot providedThe c.148C>T (p.Arg50Ter) stop…Full description
          OMIMnot providednot providedgermlinenot providednot providednot provided
          SubmitterAllele originIndividualsPhenotypes (Affected status)EthnicityGeographic originCitationsDescription

          Last Updated: Apr 21, 2017