13-48456349-G-T

Variant names:

• chr13-48456349-G-T
• rs483352690
• NM_000321.3:c.1960G>T

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000321.3(RB1):​c.1960G>T​(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 Likely pathogenic (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Pathogenic in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V654G) 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/Likely pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 5.92
• Publications: 1 publications found

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]

RB1 Gene-Disease associations (from GenCC):

• hereditary retinoblastoma

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P, Ambry Genetics
• retinoblastoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• melanoma

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 18 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 24 uncertain 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 VariationId is 100808.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 13-48456349-G-T is Pathogenic according to our data. Variant chr13-48456349-G-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 3237045.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RB1	NM_000321.3	c.1960G>T	p.Val654Leu	missense_variant, splice_region_variant	Exon 19 of 27	ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.1960G>T	p.Val654Leu	missense_variant, splice_region_variant	Exon 19 of 27		NP_001394094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.1960G>T	p.Val654Leu	missense_variant, splice_region_variant	Exon 19 of 27	1	NM_000321.3	ENSP00000267163.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Retinoblastoma Pathogenic:2

May 20, 2024

Genetic Diagnostic Laboratory, University of Pennsylvania School of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Case and Pedigree Information: BILATERAL CASES:1, UNILATERAL CASES:0, TOTAL CASES:1, PEDIGREES:1. ACMG Codes Applied:PVS1, PM2 -

May 01, 2024

Swedish National ChiCaP Initative, Genomic Medicine Sweden

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

May 03, 2025

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1960G>T pathogenic mutation (also known as p.V654L), located in coding exon 19 of the RB1 gene, results from a G to T substitution at nucleotide position 1960. This variant was reported in individuals with features consistent with RB1-related hereditary retinoblastoma (Zhang K et al. Hum Mutat, 2008 Apr;29:475-84; Hung CC et al. BMC Med Genet. 2011 May;12:76; Kugalingam N et al. BMC Med Genomics, 2023 Nov;16:279; Ambry internal data), however, it has also been reported in some unaffected family members (Zhang K et al. Hum Mutat, 2008 Apr;29:475-84; Hung CC et al. BMC Med Genet. 2011 May;12:76). 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 nucleotide position is well conserved in available vertebrate species. This amino acid position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice donor site. One RNA study reported that this variant resulted in skipping of Exon 19 (Zhang K et al. Hum Mutat. 2008 Apr;29(4):475-84). Another variant impacting the same donor site, and resulting in the same amino acid change (c.1960G>C p.V654L), has also been identified in individuals with features consistent with retinoblastoma. In addition as a missense, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this variant 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	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.68	D;.
Eigen	Uncertain	0.19
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Benign	0.042	D
MetaRNN	Uncertain	0.66	D;D
MetaSVM	Uncertain	0.18	D
MutationAssessor	Benign	0.55	N;.
PhyloP100		5.9
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
Mutation Taster		=6/94	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.22		Position offset: 0

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

Other links and lift over

dbSNP: rs483352690; hg19: chr13-49030485; COSMIC: COSV57322012; COSMIC: COSV57322012;