NM_025114.4(CEP290):c.2594_2595del (p.Leu865fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 1, 2023
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:
RCV001384273.4

Allele description [Variation Report for NM_025114.4(CEP290):c.2594_2595del (p.Leu865fs)]

NM_025114.4(CEP290):c.2594_2595del (p.Leu865fs)

Gene:
CEP290:centrosomal protein 290 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
12q21.32
Genomic location:
Preferred name:
NM_025114.4(CEP290):c.2594_2595del (p.Leu865fs)
HGVS:
  • NC_000012.12:g.88106898_88106899del
  • NG_008417.2:g.40319_40320del
  • NM_025114.4:c.2594_2595delMANE SELECT
  • NP_079390.3:p.Leu865fs
  • LRG_694t1:c.2594_2595del
  • LRG_694:g.40319_40320del
  • LRG_694p1:p.Leu865fs
  • NC_000012.11:g.88500674_88500675del
  • NC_000012.11:g.88500675_88500676del
  • NG_008417.1:g.40319_40320del
  • NM_025114.3:c.2594_2595delTC
Protein change:
L865fs
Links:
dbSNP: rs1221464366
NCBI 1000 Genomes Browser:
rs1221464366
Molecular consequence:
  • NM_025114.4:c.2594_2595del - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001583707Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 1, 2023) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis.

den Hollander AI, Koenekoop RK, Yzer S, Lopez I, Arends ML, Voesenek KE, Zonneveld MN, Strom TM, Meitinger T, Brunner HG, Hoyng CB, van den Born LI, Rohrschneider K, Cremers FP.

Am J Hum Genet. 2006 Sep;79(3):556-61. Epub 2006 Jul 11.

PubMed [citation]
PMID:
16909394
PMCID:
PMC1559533

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
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001583707.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Leu865Glnfs*9) in the CEP290 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CEP290-related conditions. ClinVar contains an entry for this variant (Variation ID: 817418). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024