NM_001379200.1(TBX1):c.1153GCCGGCGGC[1] (p.385AGG[1]) AND DiGeorge syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 6, 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:: RCV001370493.4

Allele description [Variation Report for NM_001379200.1(TBX1):c.1153GCCGGCGGC[1] (p.385AGG[1])]

NM_001379200.1(TBX1):c.1153GCCGGCGGC[1] (p.385AGG[1])

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.1153GCCGGCGGC[1] (p.385AGG[1])

HGVS:

NC_000022.11:g.19766505GCCGGCGGC[1]
NG_009229.1:g.14803GCCGGCGGC[1]
NM_001379200.1:c.1153GCCGGCGGC[1]MANE SELECT
NM_005992.1:c.1009+512_1009+520del
NM_080646.2:c.1009+512_1009+520del
NM_080647.1:c.1126GCCGGCGGC[1]
NP_001366129.1:p.385AGG[1]
NP_542378.1:p.376AGG[1]
LRG_226t1:c.1126GCCGGCGGC[1]
LRG_226:g.14803GCCGGCGGC[1]
LRG_226p1:p.376AGG[1]
NC_000022.10:g.19754028GCCGGCGGC[1]
NC_000022.10:g.19754028_19754036del
NM_080647.1:c.1135_1143del

Links:

dbSNP: rs1288296547

NCBI 1000 Genomes Browser:

rs1288296547

Molecular consequence:

NM_001379200.1:c.1153GCCGGCGGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_080647.1:c.1126GCCGGCGGC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_005992.1:c.1009+512_1009+520del - intron variant - [Sequence Ontology: SO:0001627]
NM_080646.2:c.1009+512_1009+520del - 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

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Homo sapiens isolate CHM13 chromosome 20, alternate assembly T2T-CHM13v2.0
Homo sapiens isolate CHM13 chromosome 20, alternate assembly T2T-CHM13v2.0
gi|2194972764|gnl|ASM:GCF_009914825 ef|NC_060944.1||gpp|GPC_000012759.1||gnl|NCBI_GENOMES|119580

Nucleotide
OMIM links for OMIM (Select 113705) (24)
BioSample
Protein Links for Conserved Domains (Select 112313) (188)
Protein
Taxonomy Links for GEO DataSets (Select 2374) (1)
Taxonomy
1805029[uid] (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001566995	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 6, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15060116, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001566995

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 6, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Assessment of association between variants and haplotypes of the remaining TBX1 gene and manifestations of congenital heart defects in 22q11.2 deletion patients.

Rauch A, Devriendt K, Koch A, Rauch R, Gewillig M, Kraus C, Weyand M, Singer H, Reis A, Hofbeck M.

J Med Genet. 2004 Apr;41(4):e40. No abstract available.

PubMed [citation]

PMID:: 15060116
PMCID:: PMC1735727

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, SCV001566995.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant, c.1135_1143del, results in the deletion of 3 amino acid(s) of the TBX1 protein (p.Ala379_Gly381del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has been observed in individual(s) with ventricular septal defects (PMID: 15060116). ClinVar contains an entry for this variant (Variation ID: 1060987). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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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