rs137852834
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_025114.4(CEP290):c.4723A>T(p.Lys1575*) variant causes a stop gained change. The variant allele was found at a frequency of 0.000109 in 1,590,190 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
CEP290
NM_025114.4 stop_gained
NM_025114.4 stop_gained
Scores
5
1
1
Clinical Significance
Conservation
PhyloP100: 7.08
Genes affected
CEP290 (HGNC:29021): (centrosomal protein 290) This gene encodes a protein with 13 putative coiled-coil domains, a region with homology to SMC chromosome segregation ATPases, six KID motifs, three tropomyosin homology domains and an ATP/GTP binding site motif A. The protein is localized to the centrosome and cilia and has sites for N-glycosylation, tyrosine sulfation, phosphorylation, N-myristoylation, and amidation. Mutations in this gene have been associated with Joubert syndrome and nephronophthisis and the presence of antibodies against this protein is associated with several forms of cancer. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-88083936-T-A is Pathogenic according to our data. Variant chr12-88083936-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 1339.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-88083936-T-A is described in Lovd as [Pathogenic]. Variant chr12-88083936-T-A is described in Lovd as [Likely_pathogenic]. Variant chr12-88083936-T-A is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEP290 | NM_025114.4 | c.4723A>T | p.Lys1575* | stop_gained | 36/54 | ENST00000552810.6 | NP_079390.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CEP290 | ENST00000552810.6 | c.4723A>T | p.Lys1575* | stop_gained | 36/54 | 1 | NM_025114.4 | ENSP00000448012.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152208Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000554 AC: 12AN: 216510Hom.: 0 AF XY: 0.0000857 AC XY: 10AN XY: 116644
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GnomAD4 exome AF: 0.000111 AC: 160AN: 1437982Hom.: 0 Cov.: 28 AF XY: 0.000111 AC XY: 79AN XY: 713588
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74352
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:24
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:5
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2022 | 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: 17345604, 27104957, 28829391, 17964524, 20683928, 25920555, 28497568, 28559085, 31091803, 17564967, 26766544, 28181551, 26092869, 31734136, 32208788, 32865313, 34426522, 31589614, 29398085, 25525159) - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Joubert syndrome 5 Pathogenic:3
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2007 | - - |
Pathogenic, criteria provided, single submitter | research | UW Hindbrain Malformation Research Program, University of Washington | Feb 23, 2015 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 08, 2020 | This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2. - |
CEP290-related disorder Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 17, 2023 | Variant summary: CEP290 c.4723A>T (p.Lys1575X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 5.5e-05 in 216510 control chromosomes (gnomAD). c.4723A>T has been reported in the literature as a biallelic genotype in multiple individuals affected with CEP290-Related Disorders (e.g. Perrault_2007, Halbritter_2012). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Twelve ClinVar submitters have assessed the variant since 2014: all have classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 09, 2024 | The CEP290 c.4723A>T variant is predicted to result in premature protein termination (p.Lys1575*). This variant has been reported to be causative for Leber congenital amaurosis and Joubert syndrome (Perrault et al. 2007. PubMed ID: 17345604; Bachmann-Gagescu et al. 2015. PubMed ID: 26092869; Roosing et al. 2017. PubMed ID: 28829391). This variant is reported in 0.011% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in CEP290 are expected to be pathogenic, and this variant has been classified as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/1339/). Given the evidence, we interpret c.4723A>T (p.Lys1575*) as pathogenic. - |
Leber congenital amaurosis 10 Pathogenic:2
Pathogenic, criteria provided, single submitter | research | Ocular Genomics Institute, Massachusetts Eye and Ear | Apr 08, 2021 | The CEP290 c.4723A>T variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3. Based on this evidence we have classified this variant as Pathogenic. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2007 | - - |
Retinal dystrophy Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Jul 25, 2019 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg | Jan 01, 2015 | - - |
CEP290-related ciliopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn | Nov 30, 2023 | - - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 27, 2024 | The c.4723A>T (p.K1575*) alteration, located in exon 36 (coding exon 35) of the CEP290 gene, consists of a A to T substitution at nucleotide position 4723. This changes the amino acid from a lysine (K) to a stop codon at amino acid position 1575. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the T allele has an overall frequency of 0.006% (15/247902) total alleles studied. The highest observed frequency was 0.015% (1/6510) of Other alleles. This variant has been identified in the homozygous state and in conjunction with other CEP290 variants in individuals with features consistent with CEP290-related ciliopathy; in at least one instance, the variants were identified in trans (Feldhaus, 2020; Yohe, 2020; Sallum, 2020; Skorczyk-Werner, 2020; Barny, 2019; Sheck, 2018; Duijkers, 2018; Summers, 2017; Roosing, 2017; Stone, 2017; Bachmann-Gagescu, 2015; Coppieters, 2010; Perrault, 2007). Based on the available evidence, this alteration is classified as pathogenic. - |
Senior-Loken syndrome 6 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals | Feb 01, 2019 | - - |
Blindness Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Feb 02, 2015 | - - |
Leber congenital amaurosis Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Natera, Inc. | Jul 09, 2020 | - - |
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis;C0687120:Nephronophthisis Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 04, 2024 | This sequence change creates a premature translational stop signal (p.Lys1575*) 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 present in population databases (rs137852834, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with CEP290-related disorders (PMID: 17345604, 20683928, 23188109, 25920555, 26092869, 28497568, 28829391, 29398085). ClinVar contains an entry for this variant (Variation ID: 1339). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. - |
not specified Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 08, 2017 | - - |
Bardet-Biedl syndrome 14 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 27, 2024 | - - |
Nystagmus;C1842364:Central hypotonia;C1865060:Molar tooth sign on MRI Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Mar 07, 2016 | - - |
Senior-Loken syndrome 6;C1857780:Joubert syndrome 5;C1857821:Leber congenital amaurosis 10;C1970161:Meckel syndrome, type 4;C2673874:Bardet-Biedl syndrome 14 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 15, 2024 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at