NM_031443.4(CCM2):c.55C>T (p.Arg19Ter) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Sep 20, 2023
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:: RCV000517288.4

Allele description [Variation Report for NM_031443.4(CCM2):c.55C>T (p.Arg19Ter)]

NM_031443.4(CCM2):c.55C>T (p.Arg19Ter)

Gene:

CCM2:CCM2 scaffold protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p13

Genomic location:

Preferred name:

NM_031443.4(CCM2):c.55C>T (p.Arg19Ter)

HGVS:

NC_000007.14:g.45038277C>T
NG_016295.1:g.43090C>T
NM_001029835.2:c.118C>T
NM_001167934.2:c.31-25641C>T
NM_001167935.2:c.55C>T
NM_001363458.2:c.55C>T
NM_001363459.2:c.31-25641C>T
NM_031443.4:c.55C>TMANE SELECT
NP_001025006.1:p.Arg40Ter
NP_001161407.1:p.Arg19Ter
NP_001350387.1:p.Arg19Ter
NP_113631.1:p.Arg19Ter
NP_113631.1:p.Arg19Ter
LRG_664t1:c.118C>T
LRG_664t2:c.55C>T
LRG_664:g.43090C>T
LRG_664p1:p.Arg40Ter
LRG_664p2:p.Arg19Ter
NC_000007.13:g.45077876C>T
NM_031443.3:c.55C>T
NR_030770.2:n.137C>T
p.Arg19*

Protein change:

R19*

Links:

dbSNP: rs755800734

NCBI 1000 Genomes Browser:

rs755800734

Molecular consequence:

NM_001167934.2:c.31-25641C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001363459.2:c.31-25641C>T - intron variant - [Sequence Ontology: SO:0001627]
NR_030770.2:n.137C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001029835.2:c.118C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001167935.2:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363458.2:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_031443.4:c.55C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000612715	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Aug 2, 2017)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 19088124, 24466005, 19088123, 27153162, 18300272, 23595507, 27561926, 15122722, 26467025
SCV000748184	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Sep 20, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000612715

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Aug 2, 2017)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV000748184

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Sep 20, 2023)

germline

clinical testing

Citation Link

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	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A two-hit mechanism causes cerebral cavernous malformations: complete inactivation of CCM1, CCM2 or CCM3 in affected endothelial cells.

Pagenstecher A, Stahl S, Sure U, Felbor U.

Hum Mol Genet. 2009 Mar 1;18(5):911-8. doi: 10.1093/hmg/ddn420. Epub 2008 Dec 16.

PubMed [citation]

PMID:: 19088124
PMCID:: PMC2640205

Mutation prevalence of cerebral cavernous malformation genes in Spanish patients.

Mondéjar R, Solano F, Rubio R, Delgado M, Pérez-Sempere A, González-Meneses A, Vendrell T, Izquierdo G, Martinez-Mir A, Lucas M.

PLoS One. 2014;9(1):e86286. doi: 10.1371/journal.pone.0086286.

PubMed [citation]

PMID:: 24466005
PMCID:: PMC3900513

See all PubMed Citations (9)

Details of each submission

From Athena Diagnostics, SCV000612715.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

#	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 GeneDx, SCV000748184.4

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

Description

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; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 32170606, 27153162, 24466005, 27561926, 15122722, 19088124, 23595507, 19088123, 18300272, 30701383, 31254430, 27535533, 32615293, 36629374)

#	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

Last Updated: Sep 29, 2024

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