ClinVar Miner

Submissions for variant NM_000051.4(ATM):c.6899G>C (p.Trp2300Ser)

dbSNP: rs1555119899
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000677225 SCV002198877 uncertain significance Ataxia-telangiectasia syndrome 2021-08-28 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ATM protein function. ClinVar contains an entry for this variant (Variation ID: 559541). This missense change has been observed in individual(s) with clinical features of ataxia-telangiectasia (PMID: 30888062). This variant is not present in population databases (ExAC no frequency). This sequence change replaces tryptophan with serine at codon 2300 of the ATM protein (p.Trp2300Ser). The tryptophan residue is highly conserved and there is a large physicochemical difference between tryptophan and serine.
3billion RCV000677225 SCV002521509 likely pathogenic Ataxia-telangiectasia syndrome 2022-05-22 criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. Protein truncation variants are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.85; 3Cnet: 0.95). Same nucleotide change resulting in same amino acid change has been previously reported to be associated with ATM related disorder (ClinVar ID: VCV000559541 / PMID: 30888062). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (PMID: 30888062). A different missense change at the same codon (p.Trp2300Gly) has been reported to be associated with ATM related disorder (PMID: 33098801). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP) RCV000677225 SCV000788257 likely pathogenic Ataxia-telangiectasia syndrome 2018-07-26 no assertion criteria provided clinical testing This variant (NM_000051.3:c.6899G>C) is seen in compound heterozygosity with the variant NG_009830.1(NM_000051.3):c.(2466+1_2467-1)_(8850+1_8851-1)dup in the affected child.

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