ClinVar Miner

Submissions for variant NM_002206.3(ITGA7):c.1673C>T (p.Ser558Leu)

gnomAD frequency: 0.00002  dbSNP: rs548594784
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001373653 SCV001570380 uncertain significance Congenital muscular dystrophy due to integrin alpha-7 deficiency 2024-08-13 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 558 of the ITGA7 protein (p.Ser558Leu). This variant is present in population databases (rs548594784, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with ITGA7-related conditions. ClinVar contains an entry for this variant (Variation ID: 1063777). 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 ITGA7 protein function with a negative predictive value of 80%. 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.
Revvity Omics, Revvity RCV001373653 SCV003815714 uncertain significance Congenital muscular dystrophy due to integrin alpha-7 deficiency 2019-08-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV004037580 SCV003969238 uncertain significance not specified 2023-04-24 criteria provided, single submitter clinical testing The c.1673C>T (p.S558L) alteration is located in exon 12 (coding exon 12) of the ITGA7 gene. This alteration results from a C to T substitution at nucleotide position 1673, causing the serine (S) at amino acid position 558 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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