ClinVar Miner

Submissions for variant NM_145207.3(AFG2A):c.1574A>G (p.Asn525Ser)

gnomAD frequency: 0.00001  dbSNP: rs150684555
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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 RCV001340852 SCV001534685 uncertain significance Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome 2022-04-24 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 525 of the SPATA5 protein (p.Asn525Ser). This variant is present in population databases (rs150684555, gnomAD 0.007%). 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: 1037664). 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 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.
GeneDx RCV004789536 SCV005401444 uncertain significance not provided 2024-05-13 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004978363 SCV005573495 uncertain significance Inborn genetic diseases 2024-12-03 criteria provided, single submitter clinical testing The c.1574A>G (p.N525S) alteration is located in exon 9 (coding exon 9) of the SPATA5 gene. This alteration results from a A to G substitution at nucleotide position 1574, causing the asparagine (N) at amino acid position 525 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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