ClinVar Miner

Submissions for variant NM_212482.4(FN1):c.3289G>A (p.Glu1097Lys)

gnomAD frequency: 0.00006  dbSNP: rs753807100
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV002476632 SCV002786913 uncertain significance Glomerulopathy with fibronectin deposits 2; Spondylometaphyseal dysplasia - Sutcliffe type 2021-07-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001356595 SCV004628331 likely benign not provided 2023-11-03 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356595 SCV001551808 uncertain significance not provided no assertion criteria provided clinical testing The FN1 p.Glu1097Lys variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs753807100) and in control databases in 8 of 282710 chromosomes at a frequency of 0.0000283 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: African in 4 of 24970 chromosomes (freq: 0.00016), East Asian in 1 of 19952 chromosomes (freq: 0.00005) and European (non-Finnish) in 3 of 129038 chromosomes (freq: 0.000023), but was not observed in the Latino, Ashkenazi Jewish, European (Finnish), Other, and South Asian populations. The p.Glu1097 residue is highly conserved across mammals and other organisms and three out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest an impact to the protein. The variant occurs outside of the splicing consensus sequence and three of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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