NM_025114.4(CEP290):c.7283_7286dup (p.Tyr2429Ter) AND CEP290-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 7, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV004545135.2

Allele description [Variation Report for NM_025114.4(CEP290):c.7283_7286dup (p.Tyr2429Ter)]

NM_025114.4(CEP290):c.7283_7286dup (p.Tyr2429Ter)

Genes:

RLIG1:RNA 5'-phosphate and 3'-OH ligase 1 [Gene - HGNC]
CEP290:centrosomal protein 290 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

12q21.32

Genomic location:

Preferred name:

NM_025114.4(CEP290):c.7283_7286dup (p.Tyr2429Ter)

HGVS:

NC_000012.12:g.88049340_88049343dup
NG_008417.2:g.97876_97879dup
NM_001009894.3:c.*918_*921dupMANE SELECT
NM_025114.4:c.7283_7286dupMANE SELECT
NP_079390.3:p.Tyr2429Ter
LRG_694t1:c.7283_7286dup
LRG_694:g.97876_97879dup
LRG_694p1:p.Tyr2429Ter
NC_000012.11:g.88443114_88443115insTACT
NC_000012.11:g.88443117_88443120dup
NM_025114.3:c.7283_7286dup
NM_025114.3:c.7283_7286dupAGTA

Protein change:

Y2429*

Links:

dbSNP: rs773642187

NCBI 1000 Genomes Browser:

rs773642187

Molecular consequence:

NM_001009894.3:c.*918_*921dup - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_025114.4:c.7283_7286dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: CEP290-related disorder
Synonyms:: CEP290-Related Disorders; CEP290-related condition
Identifiers:: MedGen: CN239314

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004771329	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Likely pathogenic (Feb 7, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004771329

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Likely pathogenic
(Feb 7, 2024)

germline

clinical testing

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004771329.2

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

Description

The CEP290 c.7283_7286dupAGTA variant is predicted to result in premature protein termination (p.Tyr2429*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.017% of alleles in individuals of African descent in gnomAD. Nonsense variants in CEP290 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

#	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 11, 2025

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