ClinVar Miner

Submissions for variant NM_012414.4(RAB3GAP2):c.2090A>G (p.Asn697Ser)

gnomAD frequency: 0.00001  dbSNP: rs766182343
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002873139 SCV003620444 uncertain significance Inborn genetic diseases 2022-06-08 criteria provided, single submitter clinical testing The c.2090A>G (p.N697S) alteration is located in exon 20 (coding exon 20) of the RAB3GAP2 gene. This alteration results from a A to G substitution at nucleotide position 2090, causing the asparagine (N) at amino acid position 697 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV003491280 SCV004236529 uncertain significance not provided 2023-11-07 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV005208198 SCV005849252 uncertain significance Warburg micro syndrome 2 criteria provided, single submitter clinical testing The missense c.2090A>G (p.Asn697Ser) variant in RAB3GAP2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Asn697Ser variant is present with allele frequency of 0.0008% in gnomAD Exomes. This variant has been submitted to the ClinVar database as Uncertain Significance. Multiple lines of computational evidence (Polyphen - Benign, SIFT - Tolerated and MutationTaster - Polymorphism) predict no damaging effect on protein structure and function for this variant. The reference amino acid at this position on RAB3GAP2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Asn at position 697 is changed to a Ser changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as a Variant of Uncertain Significance (VUS).

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