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NM_019892.6(INPP5E):c.473del (p.Gly158fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 1, 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:
RCV000522108.3

Allele description [Variation Report for NM_019892.6(INPP5E):c.473del (p.Gly158fs)]

NM_019892.6(INPP5E):c.473del (p.Gly158fs)

Gene:
INPP5E:inositol polyphosphate-5-phosphatase E [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.3
Genomic location:
Preferred name:
NM_019892.6(INPP5E):c.473del (p.Gly158fs)
HGVS:
  • NC_000009.12:g.136438952del
  • NG_016126.1:g.5858del
  • NM_001318502.2:c.473del
  • NM_019892.5:c.473delG
  • NM_019892.6:c.473delMANE SELECT
  • NP_001305431.1:p.Gly158fs
  • NP_063945.2:p.Gly158fs
  • NC_000009.11:g.139333399del
  • NC_000009.11:g.139333404del
  • NM_019892.4:c.473del
  • NM_019892.4:c.473delG
  • NM_019892.6:c.473del
Protein change:
G158fs
Links:
dbSNP: rs779450345
NCBI 1000 Genomes Browser:
rs779450345
Molecular consequence:
  • NM_001318502.2:c.473del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_019892.6:c.473del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000619784GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Aug 1, 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, SCV000619784.1

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

Description

A variant that is likely pathogenic has been identified in the INPP5E gene. The c.473delG variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.473delG variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The c.473delG variant causes a frameshift starting with codon Glycine 158, changes this amino acid to a Valine residue and creates a premature Stop codon at position 40 of the new reading frame, denoted p.Gly158ValfsX40. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. 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: Jun 23, 2024