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NM_001080522.2(CC2D2A):c.3289delG AND Joubert syndrome 9

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Jun 24, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000201550.19

Allele description [Variation Report for NM_001080522.2(CC2D2A):c.3289delG]

NM_001080522.2(CC2D2A):c.3289delG

Gene:
CC2D2A:coiled-coil and C2 domain containing 2A [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4p15.32
Genomic location:
Preferred name:
NM_001080522.2(CC2D2A):c.3289delG
HGVS:
  • NC_000004.12:g.15567677del
  • NG_013035.1:g.102812del
  • NM_001080522.2:c.3289delG
  • LRG_697t1:c.3289del
  • LRG_697:g.102812del
  • NC_000004.11:g.15569299del
  • NC_000004.11:g.15569300del
  • NM_001080522.2:c.3289-1del
Links:
OMIM: 612013.0006; dbSNP: rs386833751
NCBI 1000 Genomes Browser:
rs386833751
Molecular consequence:
  • NM_001080522.2:c.3289delG - splice acceptor variant - [Sequence Ontology: SO:0001574]
Functional consequence:
Unknown function
Observations:
1

Condition(s)

Name:
Joubert syndrome 9 (JBTS9)
Identifiers:
MONDO: MONDO:0012849; MedGen: C2676788; Orphanet: 2318; OMIM: 612285

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000256334UW Hindbrain Malformation Research Program, University of Washington

See additional submitters

criteria provided, single submitter

(Bachmann-Gagescu et al. (J Med Genet. 2015))
Pathogenic
(Feb 23, 2015)
unknownresearch

PubMed (1)
[See all records that cite this PMID]

SCV000593889Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 17, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001424034Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia
criteria provided, single submitter

(Perez et al. (J Hum Genet. 2020))
Pathogenicunknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001934273Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 27, 2020)
maternalclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002557629Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 24, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedmaternalyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyes1not providednot providednot providednot providedclinical testing, research

Citations

PubMed

Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity.

Bachmann-Gagescu R, Dempsey JC, Phelps IG, O'Roak BJ, Knutzen DM, Rue TC, Ishak GE, Isabella CR, Gorden N, Adkins J, Boyle EA, de Lacy N, O'Day D, Alswaid A, Ramadevi A R, Lingappa L, Lourenço C, Martorell L, Garcia-Cazorla À, Ozyürek H, Haliloğlu G, Tuysuz B, et al.

J Med Genet. 2015 Aug;52(8):514-22. doi: 10.1136/jmedgenet-2015-103087. Epub 2015 Jun 19.

PubMed [citation]
PMID:
26092869
PMCID:
PMC5082428

Overwhelming genetic heterogeneity and exhausting molecular diagnostic process in chronic and progressive ataxias: facing it up with an algorithm, a gene, a panel at a time.

Perez Maturo J, Zavala L, Vega P, González-Morón D, Medina N, Salinas V, Rosales J, Córdoba M, Arakaki T, Garretto N, Rodríguez-Quiroga S, Kauffman MA.

J Hum Genet. 2020 Oct;65(10):895-902. doi: 10.1038/s10038-020-0785-z. Epub 2020 Jun 3.

PubMed [citation]
PMID:
32488064
See all PubMed Citations (4)

Details of each submission

From UW Hindbrain Malformation Research Program, University of Washington, SCV000256334.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000593889.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Consultorio y Laboratorio de Neurogenética, Hospital JM Ramos Mejia, SCV001424034.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001934273.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was identified as compound heterozygous with NM_001080522.2:c.4786G>A.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyesnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557629.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Joubert syndrome 9, (MIM#612285); Meckel syndrome 6 (MIM#612284) and COACH syndrome (MIM#216360). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 54 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (ClinVar, DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in at least 10 individuals, two of whom diagnosed with Joubert Syndrome (ClinVar; PMID: 28125082). (SP) 1102 - Strong phenotype match for this individual. (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024