ClinVar Miner

Submissions for variant NM_022489.4(INF2):c.1316C>T (p.Pro439Leu)

gnomAD frequency: 0.00002  dbSNP: rs1375222598
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001758159 SCV001985678 uncertain significance not provided 2020-07-29 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV003771923 SCV004596577 uncertain significance Focal segmental glomerulosclerosis 5; Charcot-Marie-Tooth disease dominant intermediate E 2023-06-27 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. 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 INF2 protein function. ClinVar contains an entry for this variant (Variation ID: 1303866). This variant has not been reported in the literature in individuals affected with INF2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 439 of the INF2 protein (p.Pro439Leu).
Ambry Genetics RCV004040081 SCV004887953 likely benign Inborn genetic diseases 2024-01-12 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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