ClinVar Miner

Submissions for variant NM_031935.3(HMCN1):c.15685A>G (p.Met5229Val)

gnomAD frequency: 0.00001  dbSNP: rs748823261
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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 RCV001100285 SCV001256798 uncertain significance Age related macular degeneration 1 2018-01-12 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001856361 SCV002291464 uncertain significance not provided 2023-04-24 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 875962). This variant has not been reported in the literature in individuals affected with HMCN1-related conditions. This variant is present in population databases (rs748823261, gnomAD 0.05%). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 5229 of the HMCN1 protein (p.Met5229Val).
Genome-Nilou Lab RCV001100285 SCV004180636 uncertain significance Age related macular degeneration 1 2023-04-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV004032062 SCV004883092 uncertain significance not specified 2023-12-04 criteria provided, single submitter clinical testing The c.15685A>G (p.M5229V) alteration is located in exon 101 (coding exon 101) of the HMCN1 gene. This alteration results from a A to G substitution at nucleotide position 15685, causing the methionine (M) at amino acid position 5229 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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