NM_024665.7(TBL1XR1):c.710G>A (p.Gly237Asp) AND Pierpont syndrome

Clinical significance:Likely pathogenic (Last evaluated: Apr 1, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001175162.2

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.710G>A (p.Gly237Asp)]

NM_024665.7(TBL1XR1):c.710G>A (p.Gly237Asp)

Gene:
TBL1XR1:TBL1X receptor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q26.32
Genomic location:
Preferred name:
NM_024665.7(TBL1XR1):c.710G>A (p.Gly237Asp)
HGVS:
  • NC_000003.12:g.177047542C>T
  • NG_047195.1:g.154719G>A
  • NM_001321193.3:c.710G>A
  • NM_001321194.3:c.710G>A
  • NM_001321195.3:c.449G>A
  • NM_001374327.1:c.710G>A
  • NM_001374328.1:c.710G>A
  • NM_001374329.1:c.710G>A
  • NM_001374330.1:c.449G>A
  • NM_024665.7:c.710G>AMANE SELECT
  • NP_001308122.1:p.Gly237Asp
  • NP_001308123.1:p.Gly237Asp
  • NP_001308124.1:p.Gly150Asp
  • NP_001361256.1:p.Gly237Asp
  • NP_001361257.1:p.Gly237Asp
  • NP_001361258.1:p.Gly237Asp
  • NP_001361259.1:p.Gly150Asp
  • NP_078941.2:p.Gly237Asp
  • NC_000003.11:g.176765330C>T
  • NM_024665.5:c.710G>A
Protein change:
G150D
Molecular consequence:
  • NM_001321193.3:c.710G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321194.3:c.710G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321195.3:c.449G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374327.1:c.710G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374328.1:c.710G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374329.1:c.710G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001374330.1:c.449G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024665.7:c.710G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
probably has functional consequence
Observations:
1

Condition(s)

Name:
Pierpont syndrome (PRPTS)
Identifiers:
MONDO: MONDO:0011213; MedGen: C1865644; OMIM: 602342

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001298078Servicio Extremeño de Salud,Hospital de Méridacriteria provided, single submitter
Likely pathogenic
(Apr 1, 2020)
de novoclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Caucasiande novoyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Servicio Extremeño de Salud,Hospital de Mérida, SCV001298078.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testingnot provided

Description

The G237D variant has been discovered in a boy with MR and characteristics of Pierpont Syndrome. The mutation is a missense "de novo" mutation as all the mutations described previously in this condition, and affects a highly conserved residue in one of the eight conserved WD domains of the protein. It is not present in any of the databases consulted (1000G, esp6500, ExAC, gnomAD, Kaviar, dbSNP, HRC). The in silico algortihms used to test pathogenicity, (SIFT, PolyPhen2, LRT; Mutation Taster, Mutation Assesor) classified the variant as deleterious, and the scores for CADD, and DANN were 33 and 0.999 respectively. Also, it meets the criteria from ACMG to be classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2021

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