ClinVar Miner

Submissions for variant NM_006642.5(SDCCAG8):c.1420del (p.Glu474fs) (rs397515335)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000256021 SCV000322171 pathogenic not provided 2015-09-30 criteria provided, single submitter clinical testing The c.1420delG pathogenic variant in the SDCCAG8 gene has been reported previously in the homozygous state in two siblings with nephronophthisis and retinal dystrophy and was absent from 270 control individuals (Otto et al., 2010). The c.1420delG variant causes a frameshift starting with codon Glutamate 474, changes this amino acid to a Serine residue, and creates a premature Stop codon at position 20 of the new reading frame, denoted p.Glu474SerfsX20. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1420delG variant was not observed with any significant frequency in approximately 6,200 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.1420delG as a pathogenic variant.
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000625956 SCV000746554 pathogenic Bardet-Biedl syndrome 2017-12-03 criteria provided, single submitter clinical testing
Invitae RCV001056393 SCV001220834 pathogenic Senior-Loken syndrome 7; Bardet-Biedl syndrome 16 2019-12-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu474Serfs*20) in the SDCCAG8 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs770467138, ExAC 0.02%). This variant has been observed in individual(s) with Senior-Loken syndrome (PMID: 20835237). ClinVar contains an entry for this variant (Variation ID: 57). Loss-of-function variants in SDCCAG8 are known to be pathogenic (PMID: 20835237). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000000074 SCV000020217 pathogenic Senior-Loken syndrome 7 2010-10-01 no assertion criteria provided literature only

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