rs1064792974
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000321.3(RB1):c.37_65del(p.Ala13ThrfsTer8) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. T12T) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
RB1
NM_000321.3 frameshift
NM_000321.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.49
Genes affected
RB1 (HGNC:9884): (RB transcriptional corepressor 1) The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 580 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 13-48303947-CCGCCGCCGCTGCCGCCGCGGAACCCCCGG-C is Pathogenic according to our data. Variant chr13-48303947-CCGCCGCCGCTGCCGCCGCGGAACCCCCGG-C is described in ClinVar as [Pathogenic]. Clinvar id is 410951.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RB1 | NM_000321.3 | c.37_65del | p.Ala13ThrfsTer8 | frameshift_variant | 1/27 | ENST00000267163.6 | |
RB1 | NM_001407165.1 | c.37_65del | p.Ala13ThrfsTer8 | frameshift_variant | 1/27 | ||
RB1 | NM_001407166.1 | c.37_65del | p.Ala13ThrfsTer8 | frameshift_variant | 1/17 | ||
RB1 | NM_001407167.1 | c.37_65del | p.Ala13ThrfsTer8 | frameshift_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RB1 | ENST00000267163.6 | c.37_65del | p.Ala13ThrfsTer8 | frameshift_variant | 1/27 | 1 | NM_000321.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinoblastoma Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | May 25, 2018 | This sequence change creates a premature translational stop signal (p.Ala13Thrfs*8) in the RB1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with RB1-related disease. ClinVar contains an entry for this variant (Variation ID: 410951). Loss-of-function variants in RB1 are known to be pathogenic (PMID: 17096365). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at