ClinVar Miner

Submissions for variant NM_001378454.1(ALMS1):c.4204A>G (p.Thr1402Ala)

gnomAD frequency: 0.00012  dbSNP: rs199649563
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000229674 SCV000290085 uncertain significance Alstrom syndrome 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 1403 of the ALMS1 protein (p.Thr1403Ala). This variant is present in population databases (rs199649563, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with ALMS1-related conditions. ClinVar contains an entry for this variant (Variation ID: 240995). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Not Available"; Align-GVGD: "Not Available". The alanine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV000480638 SCV000573176 uncertain significance not provided 2023-04-17 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV000229674 SCV001712335 uncertain significance Alstrom syndrome 2021-05-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002327138 SCV002630679 likely benign Cardiovascular phenotype 2023-02-06 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Breakthrough Genomics, Breakthrough Genomics RCV000480638 SCV005187748 uncertain significance not provided criteria provided, single submitter not provided
Natera, Inc. RCV000229674 SCV001453454 likely benign Alstrom syndrome 2020-01-01 no assertion criteria provided clinical testing

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