NM_005996.4(TBX3):c.1931C>T (p.Ala644Val) AND Ulnar-mammary syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 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:: RCV002624924.3

Allele description

NM_005996.4(TBX3):c.1931C>T (p.Ala644Val)

Gene:

TBX3:T-box transcription factor 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.21

Genomic location:

Preferred name:

NM_005996.4(TBX3):c.1931C>T (p.Ala644Val)

HGVS:

NC_000012.12:g.114672082G>A
NG_008315.1:g.17083C>T
NG_126694.1:g.672G>A
NG_126695.1:g.111G>A
NM_005996.4:c.1931C>TMANE SELECT
NM_016569.4:c.1991C>T
NP_005987.3:p.Ala644Val
NP_057653.3:p.Ala664Val
NC_000012.11:g.115109887G>A

Protein change:

A644V

Molecular consequence:

NM_005996.4:c.1931C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_016569.4:c.1991C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Ulnar-mammary syndrome (UMS)
Synonyms:: Schinzel syndrome; Ulnar-mammary syndrome of Pallister; PALLISTER ULNAR-MAMMARY SYNDROME
Identifiers:: MONDO: MONDO:0008411; MedGen: C1866994; Orphanet: 3138; OMIM: 181450

Recent activity

Clear Turn Off Turn On

435-tol
435-tol

biosample

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003519670	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 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

SCV003519670

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003519670.2

#	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 alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 644 of the TBX3 protein (p.Ala644Val). This variant is present in population databases (rs762342872, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with TBX3-related conditions. ClinVar contains an entry for this variant (Variation ID: 2199468). 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 tolerated. 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: Jun 23, 2024

ClinVar

Relating variation to medicine