ClinVar Miner

Submissions for variant NM_001080522.2(CC2D2A):c.4179+1del (rs386833760)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory,University of Chicago RCV000194003 SCV000246901 pathogenic Joubert syndrome 9 2014-09-22 criteria provided, single submitter clinical testing
UW Hindbrain Malformation Research Program,University of Washington RCV000194003 SCV000256339 pathogenic Joubert syndrome 9 2015-02-23 criteria provided, single submitter research
Genetic Services Laboratory,University of Chicago RCV000049724 SCV000593890 pathogenic Meckel syndrome type 6 2014-09-04 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000725911 SCV000701189 pathogenic not provided 2016-03-14 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV000626744 SCV000747447 pathogenic Clubfoot; Encephalocele; Postaxial polydactyly type A1; Polycystic kidney dysplasia; Oligohydramnios; Microcephaly; Narrow chest 2017-01-01 criteria provided, single submitter clinical testing
Invitae RCV000696362 SCV000824920 pathogenic Joubert syndrome; Meckel-Gruber syndrome 2019-11-27 criteria provided, single submitter clinical testing This sequence change, c.4179+1del, affects a donor splice site in intron 33 of the CC2D2A gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs386833761, ExAC 0.02%). This variant has been observed on the opposite chromosome (in trans) from other pathogenic variants in an individuals affected with Joubert syndrome (PMID: 26092869) and Meckel-Gruber syndrome (PMID: 19777577). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 56312). Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CC2D2A are known to be pathogenic (PMID: 19777577). For these reasons, this variant has been classified as Pathogenic.
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV001197298 SCV001367954 pathogenic Clubfoot; Encephalocele; Polycystic kidney dysplasia; Oligohydramnios; Microcephaly; Narrow chest; Postaxial polydactyly 2016-01-01 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP3,PP4. This variant was detected in heterozygous state.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049724 SCV000082131 probable-pathogenic Meckel syndrome type 6 no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049724 SCV000082132 probable-pathogenic Meckel syndrome type 6 no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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