NM_025114.4(CEP290):c.679_680del (p.Glu227fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 23, 2020
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:: RCV001385881.6

Allele description [Variation Report for NM_025114.4(CEP290):c.679_680del (p.Glu227fs)]

NM_025114.4(CEP290):c.679_680del (p.Glu227fs)

Gene:

CEP290:centrosomal protein 290 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q21.32

Genomic location:

Preferred name:

NM_025114.4(CEP290):c.679_680del (p.Glu227fs)

HGVS:

NC_000012.12:g.88129867_88129868del
NG_008417.2:g.17350_17351del
NM_025114.4:c.679_680delMANE SELECT
NP_079390.3:p.Glu227fs
LRG_694t1:c.679_680del
LRG_694:g.17350_17351del
LRG_694p1:p.Glu227fs
NC_000012.11:g.88523643_88523644del
NC_000012.11:g.88523644_88523645del
NG_008417.1:g.17350_17351del
NM_025114.3:c.679_680delGA

Protein change:

E227fs

Links:

dbSNP: rs62640578

NCBI 1000 Genomes Browser:

rs62640578

Molecular consequence:

NM_025114.4:c.679_680del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Name:: Nephronophthisis
Synonyms:: juvenile nephronophthisis
Identifiers:: MONDO: MONDO:0019005; MedGen: C0687120; OMIM: PS256100; Human Phenotype Ontology: HP:0000090

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001585889	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 23, 2020)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 17345604, 20690115, 25377065, 28559085, 16909394, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001585889

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 23, 2020)

germline

clinical testing

PubMed (6)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Spectrum of NPHP6/CEP290 mutations in Leber congenital amaurosis and delineation of the associated phenotype.

Perrault I, Delphin N, Hanein S, Gerber S, Dufier JL, Roche O, Defoort-Dhellemmes S, Dollfus H, Fazzi E, Munnich A, Kaplan J, Rozet JM.

Hum Mutat. 2007 Apr;28(4):416.

PubMed [citation]

PMID:: 17345604

CEP290, a gene with many faces: mutation overview and presentation of CEP290base.

Coppieters F, Lefever S, Leroy BP, De Baere E.

Hum Mutat. 2010 Oct;31(10):1097-108. doi: 10.1002/humu.21337. Review.

PubMed [citation]

PMID:: 20690115

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001585889.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115, 25377065, 28559085). This variant has been observed in individual(s) with Leber congenital amaurosis (PMID: 16909394). ClinVar contains an entry for this variant (Variation ID: 99863). This sequence change creates a premature translational stop signal (p.Glu227Serfs*2) in the CEP290 gene. It is expected to result in an absent or disrupted protein product.

#	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: Mar 5, 2024

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