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NM_001039591.3(USP9X):c.172C>T (p.Pro58Ser) AND Intellectual disability, X-linked 99

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 10, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003333767.2

Allele description [Variation Report for NM_001039591.3(USP9X):c.172C>T (p.Pro58Ser)]

NM_001039591.3(USP9X):c.172C>T (p.Pro58Ser)

Gene:
USP9X:ubiquitin specific peptidase 9 X-linked [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001039591.3(USP9X):c.172C>T (p.Pro58Ser)
Other names:
p.Pro58Ser
HGVS:
  • NC_000023.11:g.41129075C>T
  • NG_012547.1:g.48441C>T
  • NM_001039590.3:c.172C>T
  • NM_001039591.3:c.172C>TMANE SELECT
  • NP_001034679.2:p.Pro58Ser
  • NP_001034680.2:p.Pro58Ser
  • NC_000023.10:g.40988328C>T
  • NM_001039590.2:c.172C>T
Protein change:
P58S
Links:
dbSNP: rs1384577833
NCBI 1000 Genomes Browser:
rs1384577833
Molecular consequence:
  • NM_001039590.3:c.172C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001039591.3:c.172C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Intellectual disability, X-linked 99 (XLID99)
Synonyms:
INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 99
Identifiers:
MONDO: MONDO:0010487; MedGen: C3806746; Orphanet: 777; OMIM: 300919

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004041596Clinical Genomics Laboratory, Stanford Medicine
no assertion criteria provided
Uncertain significance
(Sep 10, 2020) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Clinical Genomics Laboratory, Stanford Medicine, SCV004041596.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testingnot provided

Description

The p.Pro58Ser variant in the USP9X gene has not been previously reported in association with disease and is absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The USP9X gene has fewer missense variants in the general population than expected. A low rate of missense variation may suggest that this gene is intolerant to missense variation. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Pro58Ser variant is uncertain. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PM2, PP2]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jul 7, 2024