ClinVar Miner

Submissions for variant NM_018418.5(SPATA7):c.1112T>C (p.Ile371Thr)

gnomAD frequency: 0.00022  dbSNP: rs150364664
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000300527 SCV000389320 uncertain significance Retinitis pigmentosa 2018-01-13 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.
Illumina Laboratory Services, Illumina RCV001051680 SCV000389321 uncertain significance Leber congenital amaurosis 3 2018-01-13 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.
Invitae RCV001051680 SCV001215848 uncertain significance Leber congenital amaurosis 3 2022-10-13 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 371 of the SPATA7 protein (p.Ile371Thr). This variant is present in population databases (rs150364664, gnomAD 0.07%). This missense change has been observed in individual(s) with SPATA7-related conditions (PMID: 28481129). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 314786). 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 expected to disrupt SPATA7 protein function. 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.
Fulgent Genetics, Fulgent Genetics RCV001051680 SCV002792998 uncertain significance Leber congenital amaurosis 3 2021-08-09 criteria provided, single submitter clinical testing
GenomeConnect - Invitae Patient Insights Network RCV001535483 SCV001749416 not provided not provided no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 05-22-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
OMIM RCV002279721 SCV002540620 pathogenic Retinitis pigmentosa 94, variable age at onset 2022-06-28 no assertion criteria provided literature only

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