NM_001378615.1(CC2D2A):c.439-5_492dup AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 3, 2022
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:: RCV002876281.3

Allele description [Variation Report for NM_001378615.1(CC2D2A):c.439-5_492dup]

NM_001378615.1(CC2D2A):c.439-5_492dup

Gene:

CC2D2A:coiled-coil and C2 domain containing 2A [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4p15.32

Genomic location:

Preferred name:

NM_001378615.1(CC2D2A):c.439-5_492dup

HGVS:

NC_000004.12:g.15510134_15510192dup
NG_013035.1:g.45269_45327dup
NM_001080522.2:c.439-5_492dup
NM_001378615.1:c.439-5_492dupMANE SELECT
NM_001378617.1:c.292-5_345dup
LRG_697t1:c.439-5_492dup
LRG_697:g.45269_45327dup
NC_000004.11:g.15511751_15511752insACTCATATAGCCAGGGAAAGAGGTAGAAAGGACTCAACAAGAAGTTGACTCCCAAAGTT
NC_000004.11:g.15511757_15511815dup

Molecular consequence:

NM_001080522.2:c.439-5_492dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001378615.1:c.439-5_492dup - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001378617.1:c.292-5_345dup - splice acceptor variant - [Sequence Ontology: SO:0001574]

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

Recent activity

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S41 family peptidase [Metabacillus sp. B2-18]
S41 family peptidase [Metabacillus sp. B2-18]
gi|2161689555|gnl|PRJNA781797|LPC09 0|gb|UGB29112.1|

Protein
BI093_gp20 [Bacillus phage PfEFR-5]
BI093_gp20 [Bacillus phage PfEFR-5]
Gene ID:29065468

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003231214	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003231214

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 3, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003231214.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 7 of the CC2D2A gene. It does not directly change the encoded amino acid sequence of the CC2D2A protein. This variant has not been reported in the literature in individuals affected with CC2D2A-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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