NM_000276.3(OCRL):c.1040G>A (p.Gly347Glu) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Feb 4, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000424806.1

Allele description

NM_000276.3(OCRL):c.1040G>A (p.Gly347Glu)

Gene:
OCRL:OCRL inositol polyphosphate-5-phosphatase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq26.1
Genomic location:
Preferred name:
NM_000276.3(OCRL):c.1040G>A (p.Gly347Glu)
HGVS:
  • NC_000023.11:g.129562484G>A
  • NG_008638.1:g.27210G>A
  • NM_000276.3:c.1040G>A
  • NP_000267.2:p.Gly347Glu
  • NC_000023.10:g.128696461G>A
Protein change:
G347E
Links:
dbSNP: rs1057521742
NCBI 1000 Genomes Browser:
rs1057521742
Molecular consequence:
  • NM_000276.3:c.1040G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000524384GeneDxcriteria provided, single submitter
Likely pathogenic
(Feb 4, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000524384.3

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

Description

A novel G347E variant that is likely pathogenic was identified in the OCRL gene. It has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G347E variant was not observed in approximately 6500 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 G347E 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. This substitution occurs at a position that is conserved across species in a region corresponding to the acyl chain binding site of the enzyme's catalytic domain (Pirruccello and de Camilli 2012). In silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Apr 7, 2019

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