NM_024665.6(TBL1XR1):c.1048-1G>A AND Pierpont syndrome

Clinical significance:Likely pathogenic (Last evaluated: Jan 9, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000801627.1

Allele description [Variation Report for NM_024665.6(TBL1XR1):c.1048-1G>A]

NM_024665.6(TBL1XR1):c.1048-1G>A

Gene:
TBL1XR1:TBL1X receptor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q26.32
Genomic location:
Preferred name:
NM_024665.6(TBL1XR1):c.1048-1G>A
HGVS:
  • NC_000003.12:g.177038173C>T
  • NG_047195.1:g.164088G>A
  • NM_001321193.2:c.1048-1G>A
  • NM_001321194.2:c.1048-1G>A
  • NM_001321195.2:c.787-1G>A
  • NM_024665.6:c.1048-1G>A
  • NC_000003.11:g.176755961C>T
  • NM_024665.4:c.1048-1G>A
Links:
dbSNP: rs1576993734
NCBI 1000 Genomes Browser:
rs1576993734
Molecular consequence:
  • NM_001321193.2:c.1048-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321194.2:c.1048-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001321195.2:c.787-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_024665.6:c.1048-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV000941411Invitaecriteria provided, single submitter
Likely pathogenic
(Jan 9, 2019)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain.

Laskowski RA, Tyagi N, Johnson D, Joss S, Kinning E, McWilliam C, Splitt M, Thornton JM, Firth HV; DDD Study., Wright CF.

Hum Mol Genet. 2016 Mar 1;25(5):927-35. doi: 10.1093/hmg/ddv625. Epub 2016 Jan 5.

PubMed [citation]
PMID:
26740553
PMCID:
PMC4754046

Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.

O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, et al.

Science. 2012 Dec 21;338(6114):1619-22. doi: 10.1126/science.1227764. Epub 2012 Nov 15.

PubMed [citation]
PMID:
23160955
PMCID:
PMC3528801
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV000941411.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects an acceptor splice site in intron 11 of the TBL1XR1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with TBL1XR1-related conditions. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TBL1XR1 are known to be pathogenic (PMID: 23160955, 26740553, 27824329). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Oct 7, 2021

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