NM_001379200.1(TBX1):c.1500C>G (p.Asp500Glu) AND DiGeorge syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 5, 2022
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:: RCV001872225.6

Allele description [Variation Report for NM_001379200.1(TBX1):c.1500C>G (p.Asp500Glu)]

NM_001379200.1(TBX1):c.1500C>G (p.Asp500Glu)

Gene:

TBX1:T-box transcription factor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_001379200.1(TBX1):c.1500C>G (p.Asp500Glu)

HGVS:

NC_000022.11:g.19766852C>G
NG_009229.1:g.15150C>G
NM_001379200.1:c.1500C>GMANE SELECT
NM_005992.1:c.1009+850C>G
NM_080646.2:c.1009+850C>G
NM_080647.1:c.1473C>G
NP_001366129.1:p.Asp500Glu
NP_542378.1:p.Asp491Glu
LRG_226t1:c.1473C>G
LRG_226:g.15150C>G
LRG_226p1:p.Asp491Glu
NC_000022.10:g.19754375C>G

Protein change:

D491E

Links:

dbSNP: rs777213879

NCBI 1000 Genomes Browser:

rs777213879

Molecular consequence:

NM_005992.1:c.1009+850C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_080646.2:c.1009+850C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001379200.1:c.1500C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_080647.1:c.1473C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: DiGeorge syndrome
Synonyms:: Hypoplasia of thymus and parathyroid; Third and fourth pharyngeal pouch syndrome; DiGeorge anomaly; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008564; MedGen: C0012236; Orphanet: 567; OMIM: 188400

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002124334	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 5, 2022)	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

SCV002124334

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 5, 2022)

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, SCV002124334.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with TBX1-related conditions. This variant is present in population databases (rs777213879, gnomAD 0.006%). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 491 of the TBX1 protein (p.Asp491Glu).

#	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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