13-48367512-C-T

Position:

• chr13-48367512-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000321.3(RB1):​c.958C>T​(p.Arg320Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,451,222 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: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: RB1 NM_000321.3 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 3.08

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]

LOC112268118 (HGNC:):

ACMG classification

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 13-48367512-C-T is Pathogenic according to our data. Variant chr13-48367512-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 126824.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-48367512-C-T is described in Lovd as [Pathogenic]. Variant chr13-48367512-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RB1	NM_000321.3	c.958C>T	p.Arg320Ter	stop_gained	10/27	ENST00000267163.6
LOC112268118	XR_002957522.2	n.122-2536G>A		intron_variant, non_coding_transcript_variant
RB1	NM_001407165.1	c.958C>T	p.Arg320Ter	stop_gained	10/27
RB1	NM_001407166.1	c.958C>T	p.Arg320Ter	stop_gained	10/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RB1	ENST00000267163.6	c.958C>T	p.Arg320Ter	stop_gained	10/27	1	NM_000321.3	P1
RB1	ENST00000650461.1	c.958C>T	p.Arg320Ter	stop_gained	10/27

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.89e-7 AC: 1 AN: 1451222 Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1 AN XY: 721618

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.04e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Retinoblastoma Pathogenic:5

Pathogenic, criteria provided, single submitter	research	Department of Pediatrics, Memorial Sloan Kettering Cancer Center	Dec 15, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Mar 22, 2023	The RB1 c.958C>T variant is classified as pathogenic (PVS1, PM6, PS4, PM2, PM3) The RB1 c.958C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 320 (PVS1). This variant has been identified as a de novo variant in at least four unrelated patients (PMID:33456302) (PM6). The variant has been widely reported in patients with retinoblastoma, both as germline, somatic and mosaic(PMID:33456302, PMID:28575107) (PS4). This variant is absent from population databases (PM2). This variant has been detected in trans with a somatic pathogenic variant (PMID:28575107) (PM3). The variant has been reported in dbSNP (rs121913300) and in the HGMD database as disease causing (CM941205). It has been reported as Pathogenic by other diagnostic laboratories (ClinVar Variation ID: 126824) and in the RB1 variant database (LOVD RB1-000072). -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Aug 30, 2023	This sequence change creates a premature translational stop signal (p.Arg320*) in the RB1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RB1 are known to be pathogenic (PMID: 17096365). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with bilateral retinoblastoma and retinoblastoma (PMID: 7704558, 12541220, 15605413, 24225018, 24810223, 25754945, 28575107). In at least one individual the variant was observed to be de novo. This variant is also known as g.64348C>T. ClinVar contains an entry for this variant (Variation ID: 126824). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Diagnostic Laboratory, University of Pennsylvania School of Medicine	May 20, 2024	Case and Pedigree Information: BILATERAL CASES:20, UNILATERAL CASES:2, TOTAL CASES:22, PEDIGREES:22. ACMG Codes Applied:PVS1, PM2, PS4S -
Likely pathogenic, no assertion criteria provided	literature only	Database of Curated Mutations (DoCM)	Jul 14, 2015	- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Mar 22, 2023

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 in large population cohorts (gnomAD); Observed in multiple individuals with retinoblastoma (Lohmann et al., 1996; Choy et al., 2002; Alonso et al., 2005; Sagi et al., 2015; Tomar et al., 2017); This variant is associated with the following publications: (PMID: 19280657, 34190019, 8651278, 12402348, 33493472, 7704558, 28575107, 25754945, 12541220, 15605413, 27983729, 14722923, 18840911, 34308366, 34294096, 33456302, 31772335, 34277001, 34645364, 35960463, 33318192) -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 01, 2021

The p.R320* pathogenic mutation (also known as c.958C>T), located in coding exon 10 of the RB1 gene, results from a C to T substitution at nucleotide position 958. This changes the amino acid from an arginine to a stop codon within coding exon 10. This mutation has been reported in numerous individuals affected with sporadic and familial retinoblastoma both bilaterally and unilaterally (Lohmann DR et al. Am. J. Hum. Genet. 1996 May;58(5):940-9; Richter S et al. Am. J. Hum. Genet. 2003 Feb;72(2):253-69; Alonso J et al. Hum. Mutat. 2005 Jan;25(1):99; Choy KW et al. Hum. Mutat. 2002 Nov;20(5):408; Houdayer C et al. Hum. Mutat. 2004 Feb; 23(2):193-202). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.60
CADD	Pathogenic	40
DANN	Uncertain	1.0
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Uncertain	0.83	D
MutationTaster	Benign	1.0	A
Vest4		0.96
GERP RS		5.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs121913300; hg19: chr13-48941648; COSMIC: COSV57297576; COSMIC: COSV57297576;