ClinVar Miner

Submissions for variant NM_001378615.1(CC2D2A):c.3975+4_3975+7del

dbSNP: rs386833759
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
UW Hindbrain Malformation Research Program, University of Washington RCV000201729 SCV000256362 pathogenic Joubert syndrome 9 2015-02-23 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV000800604 SCV000940330 pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome 2025-01-29 criteria provided, single submitter clinical testing This sequence change falls in intron 31 of the CC2D2A gene. It does not directly change the encoded amino acid sequence of the CC2D2A protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of Joubert syndrome (PMID: 19466712, 26092869, 29146704; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.3975delA+1_3delGTA. ClinVar contains an entry for this variant (Variation ID: 217617). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049723 SCV000082130 probable-pathogenic Meckel syndrome, type 6 no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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