13-48456349-G-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000321.3(RB1):c.1960G>C(p.Val654Leu) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin Lovd. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V654A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RB1 NM_000321.3 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 5.92

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]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a region_of_interest Domain B (size 131) in uniprot entity RB_HUMAN there are 40 pathogenic changes around while only 13 benign (75%) in NM_000321.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr13-48456349-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 100808.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 13-48456349-G-C is Pathogenic according to our data. Variant chr13-48456349-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 410929.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RB1	NM_000321.3	c.1960G>C	p.Val654Leu	missense_variant, splice_region_variant	19/27	ENST00000267163.6
RB1	NM_001407165.1	c.1960G>C	p.Val654Leu	missense_variant, splice_region_variant	19/27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RB1	ENST00000267163.6	c.1960G>C	p.Val654Leu	missense_variant, splice_region_variant	19/27	1	NM_000321.3	P1
RB1	ENST00000650461.1	c.1960G>C	p.Val654Leu	missense_variant, splice_region_variant	19/27
RB1	ENST00000643064.1	c.194+74906G>C		intron_variant
RB1	ENST00000480491.1			downstream_gene_variant		5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Retinoblastoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 29, 2019

This sequence change replaces valine with leucine at codon 654 of the RB1 protein (p.Val654Leu). The valine residue is highly conserved and there is a small physicochemical difference between valine and leucine. This variant also falls at the last nucleotide of exon 19 of the RB1 coding sequence, which is part of the consensus splice site for this exon. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the c.1960G nucleotide in the RB1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 22084214, 14722923, 15884040, 18449911). This suggests that this nucleotide is clinically-significant, and that variants that disrupt this position are likely to be disease-causing. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Experimental studies have shown that this variant disrupts mRNA splicing (PMID: 18449911). This variant has been observed in individuals affected with retinoblastoma (PMID: 19280657, 15605413). ClinVar contains an entry for this variant (Variation ID: 410929). This variant is not present in population databases (ExAC no frequency). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 12, 2018

The c.1960G>C pathogenic mutation (also known as p.V654L), located in coding exon 19 of the RB1 gene, results from a G to C substitution at nucleotide position 1960. The amino acid change results in valine to leucine at codon 654, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 19, which makes it likely to have some effect on normal mRNA splicing. This mutation has been described in multiple individuals with retinoblastoma (Alonso J et al. Hum. Mutat. 2005 Jan;25(1):99; Li T et al. Int J Clin Exp Pathol 2016;9(2):2120-2126; Ambry internal data). Using two different splice site prediction tools, this alteration is predicted by ESEfinder to abolish the native splice donor site, but is predicted to weaken (but not abolish) the efficiency of the native splice donor site by BDGP. RNA studies using patient RNA have shown that both this alteration and another mutation at this nucleotide position (c.1960G>A) cause exon 19 skipping, resulting in a truncated protein (Houdayer C et al. Hum. Mutat. 2008 Jul;29(7):975-82). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
Cadd	Uncertain	25
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.68	D;.
Eigen	Uncertain	0.19
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Benign	0.052	D
MetaRNN	Uncertain	0.67	D;D
MetaSVM	Uncertain	0.18	D
MutationAssessor	Benign	0.55	N;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.76	T
PROVEAN	Benign	-1.3	N;.
REVEL	Uncertain	0.48
Sift	Benign	0.28	T;.
Sift4G	Benign	0.97	T;.
Polyphen		0.35	B;.
Vest4		0.44
MutPred		0.78		Gain of catalytic residue at Y659 (P = 0.0117);Gain of catalytic residue at Y659 (P = 0.0117);
MVP		0.97
MPC		1.3
ClinPred		0.86	D
GERP RS		6.0
Varity_R		0.58
gMVP		0.72

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.21		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.21		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs483352690; hg19: chr13-49030485; COSMIC: COSV57309017; COSMIC: COSV57309017;