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NM_005609.4(PYGM):c.2447G>A (p.Arg816His) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 11, 2017
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:
RCV000081313.13

Allele description [Variation Report for NM_005609.4(PYGM):c.2447G>A (p.Arg816His)]

NM_005609.4(PYGM):c.2447G>A (p.Arg816His)

Gene:
PYGM:glycogen phosphorylase, muscle associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q13.1
Genomic location:
Preferred name:
NM_005609.4(PYGM):c.2447G>A (p.Arg816His)
HGVS:
  • NC_000011.10:g.64746741C>T
  • NG_007574.1:g.3716G>A
  • NG_013018.1:g.18975G>A
  • NM_001164716.1:c.2183G>A
  • NM_005609.4:c.2447G>AMANE SELECT
  • NP_001158188.1:p.Arg728His
  • NP_005600.1:p.Arg816His
  • NP_005600.1:p.Arg816His
  • LRG_100:g.3716G>A
  • NC_000011.9:g.64514213C>T
  • NM_005609.2:c.2447G>A
Protein change:
R728H
Links:
dbSNP: rs139230055
NCBI 1000 Genomes Browser:
rs139230055
Molecular consequence:
  • NM_001164716.1:c.2183G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005609.4:c.2447G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000582134GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(May 11, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000582134.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the PYGM gene. The R816H variant has been previously reported as a homozygous change in a consanguineous family with non-syndromic intellectual disability; additional variants were also identified and the authors concluded that the R816H only partially contributes to the phenotype in the family. (Makrythanasis et at., 2014). The R816H variant is observed in 7/16512 (0.04%) alleles from individuals of South Asian background, (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, the R816H variant a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Nov 10, 2024