NM_001378615.1(CC2D2A):c.3084del (p.Lys1029fs) AND not provided

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 8, 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:: RCV000294687.8

Allele description [Variation Report for NM_001378615.1(CC2D2A):c.3084del (p.Lys1029fs)]

NM_001378615.1(CC2D2A):c.3084del (p.Lys1029fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

4p15.32

Genomic location:

Preferred name:

NM_001378615.1(CC2D2A):c.3084del (p.Lys1029fs)

Other names:

p.Lys1029Argfs*3

HGVS:

NC_000004.12:g.15563424del
NG_013035.1:g.98559del
NM_001080522.2:c.3084del
NM_001378615.1:c.3084delMANE SELECT
NM_001378617.1:c.2937del
NP_001073991.2:p.Lys1029fs
NP_001365544.1:p.Lys1029fs
NP_001365546.1:p.Lys980fs
LRG_697t1:c.3084del
LRG_697:g.98559del
LRG_697p1:p.Lys1029fs
NC_000004.11:g.15565046del
NC_000004.11:g.15565047del
NM_001080522.2:c.3084delG

Protein change:

K1029fs

Links:

dbSNP: rs386833749

NCBI 1000 Genomes Browser:

rs386833749

Molecular consequence:

NM_001080522.2:c.3084del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001378615.1:c.3084del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001378617.1:c.2937del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329735	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Dec 6, 2021)	germline	clinical testing	Citation Link,
SCV002016954	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 7, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004226553	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 8, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 19466712, 19777577, 27894351, 30202406, 31130284, 33486889, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000329735

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Dec 6, 2021)

germline

clinical testing

Citation Link,

SCV002016954

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 7, 2022)

germline

clinical testing

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

SCV004226553

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 8, 2022)

germline

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation spectrum of Meckel syndrome genes: one group of syndromes or several distinct groups?

Tallila J, Salonen R, Kohlschmidt N, Peltonen L, Kestilä M.

Hum Mutat. 2009 Aug;30(8):E813-30. doi: 10.1002/humu.21057.

PubMed [citation]

PMID:: 19466712
PMCID:: PMC2718326

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

See all PubMed Citations (7)

Details of each submission

From GeneDx, SCV000329735.8

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

Description

Frameshift 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; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 33543475, 29620724, 30202406, 19466712, 27894351, 21493627, 19777577, 31130284)

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

From Revvity Omics, Revvity, SCV002016954.3

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

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV004226553.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (7)

Description

PM2, PM3, PVS1

#	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		1	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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