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NM_001080522.2(CC2D2A):c.3289delG AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 24, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000817119.15

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

Condition(s)

Name:
Familial aplasia of the vermis
Synonyms:
CEREBELLOPARENCHYMAL DISORDER IV; Joubert syndrome; Cerebelloparenchymal disorder 4; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0018772; MedGen: C0431399; Orphanet: 475; OMIM: PS213300
Name:
Meckel-Gruber syndrome
Synonyms:
DYSENCEPHALIA SPLANCHNOCYSTICA; Gruber syndrome; Dysencephalia splachnocystica
Identifiers:
MONDO: MONDO:0018921; MedGen: C0265215; OMIM: PS249000

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000957664Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 24, 2024)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation.

Mougou-Zerelli S, Thomas S, Szenker E, Audollent S, Elkhartoufi N, Babarit C, Romano S, Salomon R, Amiel J, Esculpavit C, Gonzales M, Escudier E, Leheup B, Loget P, Odent S, Roume J, Gérard M, Delezoide AL, Khung S, Patrier S, Cordier MP, Bouvier R, et al.

Hum Mutat. 2009 Nov;30(11):1574-82. doi: 10.1002/humu.21116.

PubMed [citation]
PMID:
19777577
PMCID:
PMC2783384

CC2D2A is mutated in Joubert syndrome and interacts with the ciliopathy-associated basal body protein CEP290.

Gorden NT, Arts HH, Parisi MA, Coene KL, Letteboer SJ, van Beersum SE, Mans DA, Hikida A, Eckert M, Knutzen D, Alswaid AF, Ozyurek H, Dibooglu S, Otto EA, Liu Y, Davis EE, Hutter CM, Bammler TK, Farin FM, Dorschner M, Topçu M, Zackai EH, et al.

Am J Hum Genet. 2008 Nov;83(5):559-71. doi: 10.1016/j.ajhg.2008.10.002. Epub 2008 Oct 23.

PubMed [citation]
PMID:
18950740
PMCID:
PMC2668034
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000957664.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Val1097Phefs*2) in the CC2D2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CC2D2A are known to be pathogenic (PMID: 19777577). This variant is present in population databases (rs770470219, gnomAD 0.04%). This premature translational stop signal has been observed in individuals with Joubert syndrome and Meckel syndrome (PMID: 18950740, 19466712, 22241855). ClinVar contains an entry for this variant (Variation ID: 56303). 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.

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

Last Updated: May 19, 2024