ClinVar Miner

Submissions for variant NM_145207.3(AFG2A):c.1501C>T (p.Arg501Cys)

gnomAD frequency: 0.00003  dbSNP: rs370908581
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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 RCV001932044 SCV002126447 uncertain significance Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome 2022-08-09 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 501 of the SPATA5 protein (p.Arg501Cys). This variant is present in population databases (rs370908581, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with SPATA5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1361953). 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 SPATA5 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.
Ambry Genetics RCV002548041 SCV003741110 uncertain significance Inborn genetic diseases 2022-05-10 criteria provided, single submitter clinical testing The c.1501C>T (p.R501C) alteration is located in exon 9 (coding exon 9) of the SPATA5 gene. This alteration results from a C to T substitution at nucleotide position 1501, causing the arginine (R) at amino acid position 501 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GenomeConnect - Brain Gene Registry RCV003985524 SCV004801647 not provided not provided no assertion provided phenotyping only Variant classified as Uncertain significance and reported on 06-25-2021 by Invitae. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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