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NM_000169.3(GLA):c.112A>G (p.Arg38Gly) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 24, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000157892.6

Allele description [Variation Report for NM_000169.3(GLA):c.112A>G (p.Arg38Gly)]

NM_000169.3(GLA):c.112A>G (p.Arg38Gly)

Genes:
RPL36A-HNRNPH2:RPL36A-HNRNPH2 readthrough [Gene - HGNC]
GLA:galactosidase alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.1
Genomic location:
Preferred name:
NM_000169.3(GLA):c.112A>G (p.Arg38Gly)
Other names:
p.R38G:AGG>GGG
HGVS:
  • NC_000023.11:g.101407792T>C
  • NG_007119.1:g.5172A>G
  • NG_016327.1:g.4590T>C
  • NM_000169.3:c.112A>GMANE SELECT
  • NM_001199973.2:c.301-4144T>C
  • NM_001199974.2:c.178-4144T>C
  • NM_001406747.1:c.112A>G
  • NM_001406748.1:c.112A>G
  • NM_001406749.1:c.112A>G
  • NP_000160.1:p.Arg38Gly
  • NP_000160.1:p.Arg38Gly
  • NP_001393676.1:p.Arg38Gly
  • NP_001393677.1:p.Arg38Gly
  • NP_001393678.1:p.Arg38Gly
  • LRG_672t1:c.112A>G
  • LRG_672:g.5172A>G
  • LRG_672p1:p.Arg38Gly
  • NC_000023.10:g.100662780T>C
  • NM_000169.2:c.112A>G
  • NR_164783.1:n.134A>G
  • NR_176252.1:n.134A>G
  • NR_176253.1:n.134A>G
Protein change:
R38G
Links:
dbSNP: rs730880446
NCBI 1000 Genomes Browser:
rs730880446
Molecular consequence:
  • NM_001199973.2:c.301-4144T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001199974.2:c.178-4144T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000169.3:c.112A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406747.1:c.112A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406748.1:c.112A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406749.1:c.112A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164783.1:n.134A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176252.1:n.134A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176253.1:n.134A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000207823GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 20, 2014) 		germlineclinical testing

Citation Link,

SCV003816844Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Feb 24, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot 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 GeneDx, SCV000207823.10

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

Description

The R38G variant has not been published as a mutation, nor has it been reported as a benign polymorphism. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R38G variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense mutations in nearby residues (L36S, L36F, A37T, A37V, P40S, P40A, P40H, P40L, T41I) have been reported in association with Fabry disease, supporting the functional importance of this region of the protein. However, this substitution occurs at a position that is not conserved across species. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in NEUROPATHY panel(s).

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

From Revvity Omics, Revvity, SCV003816844.2

#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: Sep 29, 2024