NM_024665.7(TBL1XR1):c.1385T>C (p.Phe462Ser) AND Pierpont syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 28, 2023
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:: RCV003592226.1

Allele description [Variation Report for NM_024665.7(TBL1XR1):c.1385T>C (p.Phe462Ser)]

NM_024665.7(TBL1XR1):c.1385T>C (p.Phe462Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3q26.32

Genomic location:

Preferred name:

NM_024665.7(TBL1XR1):c.1385T>C (p.Phe462Ser)

HGVS:

NC_000003.12:g.177033002A>G
NG_047195.1:g.169259T>C
NM_001321193.3:c.1385T>C
NM_001321194.3:c.1385T>C
NM_001321195.3:c.1124T>C
NM_001374327.1:c.1385T>C
NM_001374328.1:c.1385T>C
NM_001374329.1:c.1385T>C
NM_001374330.1:c.1124T>C
NM_024665.7:c.1385T>CMANE SELECT
NP_001308122.1:p.Phe462Ser
NP_001308123.1:p.Phe462Ser
NP_001308124.1:p.Phe375Ser
NP_001361256.1:p.Phe462Ser
NP_001361257.1:p.Phe462Ser
NP_001361258.1:p.Phe462Ser
NP_001361259.1:p.Phe375Ser
NP_078941.2:p.Phe462Ser
NC_000003.11:g.176750790A>G

Protein change:

F375S

Molecular consequence:

NM_001321193.3:c.1385T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321194.3:c.1385T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001321195.3:c.1124T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374327.1:c.1385T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374328.1:c.1385T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374329.1:c.1385T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374330.1:c.1124T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024665.7:c.1385T>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
SCV004334152	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 28, 2023)	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

SCV004334152

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 28, 2023)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004334152.1

#	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 phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 462 of the TBL1XR1 protein (p.Phe462Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of TBL1XR1-related conditions (Invitae). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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: Feb 20, 2024

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