ClinVar Miner

Submissions for variant NM_001080522.2(CC2D2A):c.3084del (p.Lys1029fs) (rs386833749)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000294687 SCV000329735 pathogenic not provided 2015-12-29 criteria provided, single submitter clinical testing The c.3084delG pathogenic variant in the CC2D2A gene has been reported previously in association with Meckel-Gruber syndrome, when present in the homozygous state or when in trans with another pathogenic variant (Tallila et al., 2009; Mougou-Zerelli et al., 2009; Hopp et al., 2011). The c.3084delG variant causes a frameshift starting with codon Lysine 1029, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 3 of the new reading frame, denoted p.Lys1029ArgfsX3. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3084delG variant was not observed 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.3084delG as a pathogenic variant.
Invitae RCV001060313 SCV001224993 pathogenic Joubert syndrome; Meckel-Gruber syndrome 2019-12-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys1029Argfs*3) in the CC2D2A gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs764571764, ExAC 0.03%). This variant has been observed in individual(s) with Meckel syndrome (PMID: 19466712, 27894351). ClinVar contains an entry for this variant (Variation ID: 56301). Loss-of-function variants in CC2D2A are known to be pathogenic (PMID: 19777577). For these reasons, this variant has been classified as Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049713 SCV000082120 probable-pathogenic Meckel syndrome type 6 no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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