ClinVar Miner

Submissions for variant NM_031935.3(HMCN1):c.6239G>C (p.Arg2080Thr)

gnomAD frequency: 0.00009  dbSNP: rs199945360
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000283753 SCV000351856 uncertain significance Age related macular degeneration 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV001850503 SCV002197176 uncertain significance not provided 2023-11-18 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with threonine, which is neutral and polar, at codon 2080 of the HMCN1 protein (p.Arg2080Thr). This variant is present in population databases (rs199945360, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with HMCN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 294172). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.
Ambry Genetics RCV003165789 SCV003863967 uncertain significance Inborn genetic diseases 2023-02-16 criteria provided, single submitter clinical testing The c.6239G>C (p.R2080T) alteration is located in exon 40 (coding exon 40) of the HMCN1 gene. This alteration results from a G to C substitution at nucleotide position 6239, causing the arginine (R) at amino acid position 2080 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV000283753 SCV004179797 uncertain significance Age related macular degeneration 1 2023-04-11 criteria provided, single submitter clinical testing

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