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NM_000276.4(OCRL):c.25G>A (p.Ala9Thr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 17, 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:
RCV000482529.1

Allele description [Variation Report for NM_000276.4(OCRL):c.25G>A (p.Ala9Thr)]

NM_000276.4(OCRL):c.25G>A (p.Ala9Thr)

Genes:
OCRL:OCRL inositol polyphosphate-5-phosphatase [Gene - OMIM - HGNC]
LOC113875008:Sharpr-MPRA regulatory region 13828 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq26.1
Genomic location:
Preferred name:
NM_000276.4(OCRL):c.25G>A (p.Ala9Thr)
HGVS:
  • NC_000023.11:g.129540464G>A
  • NG_008638.1:g.5190G>A
  • NG_063196.1:g.473G>A
  • NM_000276.4:c.25G>AMANE SELECT
  • NM_001318784.2:c.25G>A
  • NM_001587.4:c.25G>A
  • NP_000267.2:p.Ala9Thr
  • NP_001305713.1:p.Ala9Thr
  • NP_001578.2:p.Ala9Thr
  • NC_000023.10:g.128674441G>A
  • NM_000276.3:c.25G>A
Protein change:
A9T
Links:
dbSNP: rs1064796554
NCBI 1000 Genomes Browser:
rs1064796554
Molecular consequence:
  • NM_000276.4:c.25G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318784.2:c.25G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001587.4:c.25G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000573374GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Feb 17, 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, SCV000573374.3

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

Description

The A9T variant in the OCRL gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The A9T variant is not observed in large population cohorts; however, limited data are available (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A9T 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 not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret A9T as a variant of uncertain significance.

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

Last Updated: Oct 14, 2023