ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.9589T>A (p.Ser3197Thr) (rs369682692)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD, LLC RCV000595407 SCV000705445 uncertain significance not provided 2017-02-15 criteria provided, single submitter clinical testing
Counsyl RCV000664857 SCV000788878 uncertain significance Alstrom syndrome 2017-03-22 criteria provided, single submitter clinical testing
Invitae RCV000664857 SCV000942023 uncertain significance Alstrom syndrome 2019-11-13 criteria provided, single submitter clinical testing This sequence change replaces serine with threonine at codon 3198 of the ALMS1 protein (p.Ser3198Thr). The serine residue is moderately conserved and there is a small physicochemical difference between serine and threonine. This variant is present in population databases (rs369682692, ExAC 0.04%). This variant has been observed along with two other variants in the same ALMS1 gene in individuals with clinical features of ALMS1-related disease (PMID: 25468891, Invitae). This variant is also known as c.9586T>A, p.Ser3196Thr in the literature. ClinVar contains an entry for this variant (Variation ID: 499779). 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
GeneDx RCV000595407 SCV001789704 uncertain significance not provided 2020-11-27 criteria provided, single submitter clinical testing Reported previously as S3196T using alternate nomenclature, this variant was observed in the presence of two other ALMS1 variants, phase unknown, in a patient of Puerto Rican background with congenital hearing loss, retinitis pigmentosa, delalyed walking, and a clinical diagnosis of Usher syndrome type I (Bujakowska et al., 2014); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 25468891)

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