NM_001039591.3(USP9X):c.517CTT[1] (p.Leu174del) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 24, 2016
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:
RCV000413770.1

Allele description

NM_001039591.3(USP9X):c.517CTT[1] (p.Leu174del)

Gene:
USP9X:ubiquitin specific peptidase 9 X-linked [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001039591.3(USP9X):c.517CTT[1] (p.Leu174del)
HGVS:
  • NC_000023.11:g.41136885CTT[1]
  • NG_012547.1:g.56251CTT[1]
  • NM_001039590.3:c.517CTT[1]
  • NM_001039591.3:c.517CTT[1]MANE SELECT
  • NP_001034679.2:p.Leu174del
  • NP_001034680.2:p.Leu174del
  • NC_000023.10:g.40996138CTT[1]
  • NM_001039590.2:c.520_522delCTT
Protein change:
L174del
Links:
dbSNP: rs1057518114
NCBI 1000 Genomes Browser:
rs1057518114
Molecular consequence:
  • NM_001039590.3:c.517CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001039591.3:c.517CTT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000491524GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jun 24, 2016) 		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, SCV000491524.2

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

Description

The c.520_522delCTT variant in the USP9X gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The c.520_522delCTT variant results in an in-frame, 3 base pair deletion and is predicted to cause loss of a Leucine residue at position 174 in the protein, denoted as p.Leu174del. In-frame deletions frequently impact the resultant protein as missense changes do. Missense variants and an one in-frame deletion have been reported in the Human Gene Mutation Database in association with USP9X-related disorders (Stenson et al., 2014). The c.520_522delCTT 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. This substitution occurs at a position that is conserved across species. Therefore, we interpret c.520_522delCTT as a likely pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

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

Last Updated: Apr 23, 2022