ClinVar Miner

Submissions for variant NM_002206.3(ITGA7):c.1625G>A (p.Arg542His)

gnomAD frequency: 0.00007  dbSNP: rs17854598
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519970 SCV000617971 uncertain significance not provided 2017-10-30 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the ITGA7 gene. The R542H variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R542H variant is observed in 2/24012 (0.01%) alleles from individuals of African background (Lek et al., 2016). The R542H variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species; and in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000704244 SCV000833185 uncertain significance Congenital muscular dystrophy due to integrin alpha-7 deficiency 2022-03-26 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 449648). This variant has not been reported in the literature in individuals affected with ITGA7-related conditions. This variant is present in population databases (rs17854598, gnomAD 0.008%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 542 of the ITGA7 protein (p.Arg542His).
Revvity Omics, Revvity RCV000704244 SCV003815726 uncertain significance Congenital muscular dystrophy due to integrin alpha-7 deficiency 2021-06-01 criteria provided, single submitter clinical testing

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