NM_024665.7(TBL1XR1):c.787G>A (p.Gly263Arg) AND Pierpont syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 7, 2021
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:: RCV001959832.6

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.787G>A (p.Gly263Arg)]

NM_024665.7(TBL1XR1):c.787G>A (p.Gly263Arg)

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.787G>A (p.Gly263Arg)

HGVS:

NC_000003.12:g.177047377C>T
NG_047195.1:g.154884G>A
NM_001321193.3:c.787G>A
NM_001321194.3:c.787G>A
NM_001321195.3:c.526G>A
NM_001374327.1:c.787G>A
NM_001374328.1:c.787G>A
NM_001374329.1:c.787G>A
NM_001374330.1:c.526G>A
NM_024665.7:c.787G>AMANE SELECT
NP_001308122.1:p.Gly263Arg
NP_001308123.1:p.Gly263Arg
NP_001308124.1:p.Gly176Arg
NP_001361256.1:p.Gly263Arg
NP_001361257.1:p.Gly263Arg
NP_001361258.1:p.Gly263Arg
NP_001361259.1:p.Gly176Arg
NP_078941.2:p.Gly263Arg
NC_000003.11:g.176765165C>T

Protein change:

G176R

Links:

dbSNP: rs2108479602

NCBI 1000 Genomes Browser:

rs2108479602

Molecular consequence:

NM_001321193.3:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001321194.3:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001321195.3:c.526G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374327.1:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374328.1:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374329.1:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374330.1:c.526G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024665.7:c.787G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002216555	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 7, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002216555

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 7, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002216555.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TBL1XR1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with TBL1XR1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with arginine at codon 263 of the TBL1XR1 protein (p.Gly263Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine.

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

Last Updated: Sep 29, 2024

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