rs370880399

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_001378615.1(CC2D2A):c.3055C>T(p.Arg1019Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000591 in 1,606,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000056 ( 0 hom. )

Consequence

CC2D2A
NM_001378615.1 stop_gained

Scores

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9

Conservation

PhyloP100: 4.82

Variant links:

Genes affected

CC2D2A (HGNC:29253): (coiled-coil and C2 domain containing 2A) This gene encodes a coiled-coil and calcium binding domain protein that appears to play a critical role in cilia formation. Mutations in this gene cause Meckel syndrome type 6, as well as Joubert syndrome type 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

CC2D2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 4-15563395-C-T is Pathogenic according to our data. Variant chr4-15563395-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 217602.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-15563395-C-T is described in Lovd as [Pathogenic]. Variant chr4-15563395-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CC2D2A	NM_001378615.1 linkuse as main transcript	c.3055C>T	p.Arg1019Ter	stop_gained	24/37	ENST00000424120.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CC2D2A	ENST00000424120.6 linkuse as main transcript	c.3055C>T	p.Arg1019Ter	stop_gained	24/37	5	NM_001378615.1	P1	Q9P2K1-4

Frequencies

GnomAD3 genomes

AF:

0.0000920

AC:

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000724

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000480

GnomAD3 exomes

AF:

0.000102

AC:

AN:

236182

Hom.:

AF XY:

0.0000940

AC XY:

AN XY:

127678

show subpopulations

Gnomad AFR exome

AF:

0.0000696

Gnomad AMR exome

AF:

0.0000605

Gnomad ASJ exome

AF:

0.00133

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000346

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000470

Gnomad OTH exome

AF:

0.000343

GnomAD4 exome

AF:

0.0000557

AC:

AN:

1454594

Hom.:

Cov.:

AF XY:

0.0000650

AC XY:

AN XY:

722708

show subpopulations

Gnomad4 AFR exome

AF:

0.0000899

Gnomad4 AMR exome

AF:

0.0000920

Gnomad4 ASJ exome

AF:

0.00154

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000236

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000144

Gnomad4 OTH exome

AF:

0.000249

GnomAD4 genome

AF:

0.0000920

AC:

AN:

152154

Hom.:

Cov.:

AF XY:

0.0000807

AC XY:

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.0000724

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000480

Alfa

AF:

0.000195

Hom.:

Bravo

AF:

0.0000945

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.000260

AC:

ESP6500EA

AF:

0.000241

AC:

ExAC

AF:

0.0000993

AC:

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Joubert syndrome 9

Pathogenic:3

Pathogenic, criteria provided, single submitter	research	UW Hindbrain Malformation Research Program, University of Washington	Feb 23, 2015	- -
Pathogenic, criteria provided, single submitter	research	Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL)	Apr 27, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	May 28, 2021	- -

not provided

Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The CC2D2A p.R1019* variant was identified in the heterozygous or compound heterozygous state in 4 of 194 families with Joubert syndrome and related disorders (Gorden_2008_PMID:18950740; Bachmann-Gagescu_2012_PMID:22241855). The variant was identified in dbSNP (ID: rs370880399) and ClinVar (classified as pathogenic by Invitae, GeneDx, Fulgent Genetics, UW Hindbrain Malformation Research Program, University of Washington and as likely pathogenic by Illumina). The variant was identified in control databases in 26 of 267576 chromosomes at a frequency of 0.00009717 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 14 of 10098 chromosomes (freq: 0.001386), Other in 2 of 6912 chromosomes (freq: 0.000289), African in 2 of 23072 chromosomes (freq: 0.000087), Latino in 2 of 33894 chromosomes (freq: 0.000059), European (non-Finnish) in 5 of 121798 chromosomes (freq: 0.000041) and South Asian in 1 of 28914 chromosomes (freq: 0.000035), but was not observed in the East Asian or European (Finnish) populations. The c.3055C>T variant leads to a premature stop codon at position 1019 which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the CC2D2A gene are an established mechanism of disease in Joubert syndrome and related disorders and is the type of variant expected to cause the disorder when found in the homozygous or compound heterozygous state. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratoryâ€šÃ„Ã´s criteria to be classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 31, 2022	Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 27081510, 19466712, 22241855, 26092869, 31589614, 33486889, 18950740, 29165578) -

Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 11, 2024

This sequence change creates a premature translational stop signal (p.Arg1019*) 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 (rs370880399, gnomAD 0.2%). This premature translational stop signal has been observed in individual(s) with Joubert syndrome (PMID: 18950740, 22241855, 26092869, 27082236). ClinVar contains an entry for this variant (Variation ID: 217602). For these reasons, this variant has been classified as Pathogenic. -

CC2D2A-related condition

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 14, 2023

The CC2D2A c.3055C>T variant is predicted to result in premature protein termination (p.Arg1019*). This variant has been reported in multiple individuals with Joubert syndrome (Gorden et al. 2008. PubMed ID: 18950740; Bachmann-Gagescu et al. 2015. PubMed ID: 26092869). We have also detected this variant in the compound heterozygous state in a child with Joubert syndrome (internal data, PreventionGenetics). Taken together, we interpret this variant as pathogenic. -

Joubert syndrome 9;C2676790:Meckel syndrome, type 6;C5435651:COACH syndrome 1

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

CC2D2A-Related Disorders

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Nov 30, 2018

The CC2D2A c.3055C>T (p.Arg1019Ter) variant is a stop-gained variant that is predicted to cause premature truncation of the protein. This variant has been identified in at least four probands with Joubert syndrome, including in three in a compound heterozygous state with a missense variant and in one in a heterozygous state where a second variant was not detected (Gorden et al. 2008; Bachmann-Gagescu et al. 2012; Bachmann-Gagescu et al. 2015). The p.Arg1019Ter variant has also been reported in a homozygous state as a result of a different nucleotide substitution in one individual with Joubert syndrome (Ben-Salem et al. 2014). Control data are unavailable for this variant which is reported at a frequency of 0.00025 in the total population of the Exome Sequencing Project. Based on the evidence and due to the potential impact of stop-gained variants, the p.Arg1019Ter variant is classified as likely pathogenic for CC2D2A-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.47

BayesDel_noAF

Pathogenic

0.62

Cadd

Pathogenic

Dann

Uncertain

1.0

Eigen

Pathogenic

0.85

Eigen_PC

Pathogenic

0.72

FATHMM_MKL

Uncertain

0.96

MutationTaster

Benign

1.0

A;A;A;A

Vest4

0.93

GERP RS

4.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over