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NM_001379200.1(TBX1):c.1465TCG[1] (p.Ser490del) AND DiGeorge syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 22, 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:
RCV003067324.2

Allele description [Variation Report for NM_001379200.1(TBX1):c.1465TCG[1] (p.Ser490del)]

NM_001379200.1(TBX1):c.1465TCG[1] (p.Ser490del)

Gene:
TBX1:T-box transcription factor 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
22q11.21
Genomic location:
Preferred name:
NM_001379200.1(TBX1):c.1465TCG[1] (p.Ser490del)
HGVS:
  • NC_000022.11:g.19766817TCG[1]
  • NG_009229.1:g.15115TCG[1]
  • NM_001379200.1:c.1465TCG[1]MANE SELECT
  • NM_005992.1:c.1009+818_1009+820del
  • NM_080646.2:c.1009+818_1009+820del
  • NM_080647.1:c.1438TCG[1]
  • NP_001366129.1:p.Ser490del
  • NP_542378.1:p.Ser481del
  • LRG_226t1:c.1438TCG[1]
  • LRG_226:g.15115TCG[1]
  • LRG_226p1:p.Ser481del
  • NC_000022.10:g.19754340TCG[1]
  • NC_000022.10:g.19754340_19754342del
Protein change:
S481del
Molecular consequence:
  • NM_001379200.1:c.1465TCG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_080647.1:c.1438TCG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_005992.1:c.1009+818_1009+820del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_080646.2:c.1009+818_1009+820del - intron variant - [Sequence Ontology: SO:0001627]

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

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003453991Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003453991.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with TBX1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant, c.1441_1443del, results in the deletion of 1 amino acid(s) of the TBX1 protein (p.Ser481del), but otherwise preserves the integrity of the reading frame.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 20, 2024