rs1555468632
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPP5_Moderate
The NM_001042432.2(CLN3):c.461-279_677+384del variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 31)
Consequence
CLN3
NM_001042432.2 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_001042432.2 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.13
Genes affected
CLN3 (HGNC:2074): (CLN3 lysosomal/endosomal transmembrane protein, battenin) This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.108580105 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
PP5
?
Variant 16-28485962-AAGATTGCAATCATAATCAAGTTTTCTTTTCTTTCTTTTTTTTTTTTTCTTCCTGAGACAGAGTCTAACTCTGTCGCCCGGGCTGGAGTGCAATGGCACGATCTCGGCTCACTGCCACCACTGCCTCCGGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCTGAGTAGTTGGGACTACAGGCACCCGCCACCACACCTGGCTAATTGTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTTCCTGACCTTAGGCGATCTGCCCTCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACACCCAGCCATGGCCAAGTTTTCTCTCCTTGGACCCCTCTCCCTCCCGGCTCAGGGCAGCTCACCTGGCCAGCAGCAGGGCAGGGATACCCAGCATGGACAGCAGGGTCTGCTGAGGGGAGAGGCCGGCCTGGGTGAGGCCCAGGTAGGACAGGGCCCCCAGCAGCCCAGCTCCCCCAGTCCCTGAGGACCACCAGGAGATCACGGCCCTGGGAAGGAGAACACAGGAACATTCAGGAGGACCTAGGCTGACCATGGGACAGCCTCTCCCCACACTCCCTGCTCCACCTGCTTACCTGGGGTAGAAGGCAGTGAGGGAGAGGAAGGTGACCTCCCCAAGGCCTGATGAGATGCTAGCGAAGACCACACCTGGGGGGAGGACAAGCACTGGGATGGTCACACCACACCTTGCCACACTGCCCAGGCCTCTAATGTGTCTGGCCATGGCCTCCTCAGTATCAGCTCATAGAGGCTCCAATAGATCCCATGCATAGGCCAGGTTCCAGGTCTGAAGCAGAGCCCCACTCCCCTGCGTGTCCCTTCATGGAGAGTGGCACCTCCATCCACCCAGTTATCAGACCAGGGGCAGACATGCACCCTTGATGTCTCTGCCCCTTCATCAGTCTTTTTCTTTTCTTTTCTTTTTGG-A is Pathogenic according to our data. Variant chr16-28485962-AAGATTGCAATCATAATCAAGTTTTCTTTTCTTTCTTTTTTTTTTTTTCTTCCTGAGACAGAGTCTAACTCTGTCGCCCGGGCTGGAGTGCAATGGCACGATCTCGGCTCACTGCCACCACTGCCTCCGGGGTTCAAGCGATTCTCCTGCCTTAGCCTCCTGAGTAGTTGGGACTACAGGCACCCGCCACCACACCTGGCTAATTGTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTTTCCTGACCTTAGGCGATCTGCCCTCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACACCCAGCCATGGCCAAGTTTTCTCTCCTTGGACCCCTCTCCCTCCCGGCTCAGGGCAGCTCACCTGGCCAGCAGCAGGGCAGGGATACCCAGCATGGACAGCAGGGTCTGCTGAGGGGAGAGGCCGGCCTGGGTGAGGCCCAGGTAGGACAGGGCCCCCAGCAGCCCAGCTCCCCCAGTCCCTGAGGACCACCAGGAGATCACGGCCCTGGGAAGGAGAACACAGGAACATTCAGGAGGACCTAGGCTGACCATGGGACAGCCTCTCCCCACACTCCCTGCTCCACCTGCTTACCTGGGGTAGAAGGCAGTGAGGGAGAGGAAGGTGACCTCCCCAAGGCCTGATGAGATGCTAGCGAAGACCACACCTGGGGGGAGGACAAGCACTGGGATGGTCACACCACACCTTGCCACACTGCCCAGGCCTCTAATGTGTCTGGCCATGGCCTCCTCAGTATCAGCTCATAGAGGCTCCAATAGATCCCATGCATAGGCCAGGTTCCAGGTCTGAAGCAGAGCCCCACTCCCCTGCGTGTCCCTTCATGGAGAGTGGCACCTCCATCCACCCAGTTATCAGACCAGGGGCAGACATGCACCCTTGATGTCTCTGCCCCTTCATCAGTCTTTTTCTTTTCTTTTCTTTTTGG-A is described in ClinVar as [Pathogenic]. Clinvar id is 438235.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLN3 | NM_001042432.2 | c.461-279_677+384del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 8/16 | ENST00000636147.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLN3 | ENST00000636147.2 | c.461-279_677+384del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 8/16 | 1 | NM_001042432.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinitis pigmentosa Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | - | - - |
Neuronal ceroid lipofuscinosis 3 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 06, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at