ClinVar Miner

Submissions for variant NM_000316.3(PTH1R):c.1255G>A (p.Val419Ile)

gnomAD frequency: 0.00005  dbSNP: rs758673796
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000318055 SCV000444793 benign Metaphyseal chondrodysplasia, Jansen type 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Laboratory Services, Illumina RCV000377198 SCV000444794 uncertain significance Chondrodysplasia Blomstrand type 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.
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000714732 SCV000845460 uncertain significance not provided 2018-08-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001084 SCV001158218 uncertain significance not specified 2019-02-15 criteria provided, single submitter clinical testing The p.Val419Ile variant (rs758673796) has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the Genome Aggregation Database (gnomAD) with a frequency of 0.03 percent in the East Asian population (identified on 5 out of 18,854 chromosomes) and has been reported to the ClinVar database (Variation ID: 345594). The valine at position 419 is highly conserved and computational analyses of the effects of the p.Val419Ile variant on protein structure and function provides conflicting results (SIFT: tolerated, PolyPhen-2: probably damaging). Altogether, there is not enough evidence to classify the p.Val419Ile variant with certainty.
Invitae RCV000714732 SCV002230262 uncertain significance not provided 2022-11-24 criteria provided, single submitter clinical testing This variant is present in population databases (rs758673796, gnomAD 0.03%). 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 not expected to disrupt PTH1R protein function. ClinVar contains an entry for this variant (Variation ID: 345594). This variant has not been reported in the literature in individuals affected with PTH1R-related conditions. This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 419 of the PTH1R protein (p.Val419Ile).

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