NM_024665.7(TBL1XR1):c.712A>C (p.Thr238Pro) AND Pierpont syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 12, 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:: RCV001880383.6

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.712A>C (p.Thr238Pro)]

NM_024665.7(TBL1XR1):c.712A>C (p.Thr238Pro)

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.712A>C (p.Thr238Pro)

HGVS:

NC_000003.12:g.177047540T>G
NG_047195.1:g.154721A>C
NM_001321193.3:c.712A>C
NM_001321194.3:c.712A>C
NM_001321195.3:c.451A>C
NM_001374327.1:c.712A>C
NM_001374328.1:c.712A>C
NM_001374329.1:c.712A>C
NM_001374330.1:c.451A>C
NM_024665.7:c.712A>CMANE SELECT
NP_001308122.1:p.Thr238Pro
NP_001308123.1:p.Thr238Pro
NP_001308124.1:p.Thr151Pro
NP_001361256.1:p.Thr238Pro
NP_001361257.1:p.Thr238Pro
NP_001361258.1:p.Thr238Pro
NP_001361259.1:p.Thr151Pro
NP_078941.2:p.Thr238Pro
NC_000003.11:g.176765328T>G

Protein change:

T151P

Links:

dbSNP: rs1716484332

NCBI 1000 Genomes Browser:

rs1716484332

Molecular consequence:

NM_001321193.3:c.712A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321194.3:c.712A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321195.3:c.451A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374327.1:c.712A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374328.1:c.712A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374329.1:c.712A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374330.1:c.451A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024665.7:c.712A>C - 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
SCV002125329	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 12, 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

SCV002125329

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 12, 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, SCV002125329.3

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

Description

This sequence change replaces threonine with proline at codon 238 of the TBL1XR1 protein (p.Thr238Pro). The threonine residue is highly conserved and there is a small physicochemical difference between threonine and proline. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with TBL1XR1-related conditions. 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 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.

#	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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