ClinVar Miner

Submissions for variant NM_002206.3(ITGA7):c.3118G>T (p.Val1040Phe)

gnomAD frequency: 0.00001  dbSNP: rs764565180
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000482808 SCV000573689 uncertain significance not provided 2017-03-06 criteria provided, single submitter clinical testing The V1040F variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The V1040F variant is observed in 5/66712 (0.01%) alleles from individuals of European background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position where amino acids with similar properties to Valine are tolerated across species. However, this variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. Additionally, in silico analysis predicts this variant is probably damaging to the protein structure/function.
Invitae RCV000692087 SCV000819894 uncertain significance Congenital muscular dystrophy due to integrin alpha-7 deficiency 2022-06-16 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 1040 of the ITGA7 protein (p.Val1040Phe). This variant is present in population databases (rs764565180, gnomAD 0.006%). 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: 423926). 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: "Benign"; Align-GVGD: "Class C0"). 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 RCV003258824 SCV003944683 uncertain significance Inborn genetic diseases 2023-03-20 criteria provided, single submitter clinical testing The c.3118G>T (p.V1040F) alteration is located in exon 24 (coding exon 24) of the ITGA7 gene. This alteration results from a G to T substitution at nucleotide position 3118, causing the valine (V) at amino acid position 1040 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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