rs1555295354

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PP5_Very_Strong

The NM_000321.3(RB1):​c.2663G>A​(p.Ser888Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: not found (cov: 32)

Consequence

RB1
NM_000321.3 missense, splice_region

Scores

3
9
7
Splicing: ADA: 1.000
2

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:2

Conservation

PhyloP100: 9.04
Variant links:
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.

PM1
In a region_of_interest Domain C; mediates interaction with E4F1 (size 157) in uniprot entity RB_HUMAN there are 8 pathogenic changes around while only 0 benign (100%) in NM_000321.3
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 13-48476843-G-A is Pathogenic according to our data. Variant chr13-48476843-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 527935.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RB1NM_000321.3 linkuse as main transcriptc.2663G>A p.Ser888Asn missense_variant, splice_region_variant 25/27 ENST00000267163.6 NP_000312.2 P06400A0A024RDV3
RB1NM_001407165.1 linkuse as main transcriptc.2663G>A p.Ser888Asn missense_variant, splice_region_variant 25/27 NP_001394094.1
RB1NM_001407168.1 linkuse as main transcriptc.113G>A p.Ser38Asn missense_variant, splice_region_variant 2/4 NP_001394097.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RB1ENST00000267163.6 linkuse as main transcriptc.2663G>A p.Ser888Asn missense_variant, splice_region_variant 25/271 NM_000321.3 ENSP00000267163.4 P06400

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Retinoblastoma Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 13, 2023This sequence change affects codon 888 of the RB1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the RB1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with retinoblastoma (PMID: 24225018, 27879208, 34190019; Invitae). ClinVar contains an entry for this variant (Variation ID: 527935). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 25 and introduces a premature termination codon (PMID: 27879208). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitterclinical testingArcensusFeb 01, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.017
T
BayesDel_noAF
Benign
-0.26
CADD
Pathogenic
33
DANN
Uncertain
1.0
DEOGEN2
Benign
0.41
T;.
Eigen
Pathogenic
0.77
Eigen_PC
Pathogenic
0.80
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.86
D;D
M_CAP
Uncertain
0.12
D
MetaRNN
Uncertain
0.51
D;D
MetaSVM
Uncertain
0.38
D
MutationAssessor
Benign
1.1
L;.
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-1.0
N;.
REVEL
Pathogenic
0.79
Sift
Uncertain
0.010
D;.
Sift4G
Uncertain
0.020
D;.
Polyphen
0.95
P;.
Vest4
0.38
MutPred
0.35
Gain of catalytic residue at L891 (P = 0.0021);Gain of catalytic residue at L891 (P = 0.0021);
MVP
0.78
MPC
1.0
ClinPred
0.88
D
GERP RS
5.8
Varity_R
0.37
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.99
SpliceAI score (max)
0.76
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.76
Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555295354; hg19: chr13-49050979; API