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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Apr 1, 2020
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:: RCV001175162.3

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

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

Genes:

TBL1XR1:TBL1X/Y related 1 [Gene - OMIM - HGNC]
TBL1XR1-AS1:TBL1XR1 antisense RNA 1 [Gene - 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

Links:

dbSNP: rs1716484744

NCBI 1000 Genomes Browser:

rs1716484744

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:

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001298078	Servicio Extremeño de Salud, Hospital de Mérida	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 1, 2020)	de novo	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001298078

Servicio Extremeño de Salud, Hospital de Mérida

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 1, 2020)

de novo

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
Caucasian	de novo	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Caucasian	1	not provided	not provided	clinical testing	not 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	de novo	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jun 23, 2024

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