NM_000321.3:c.1060_1061delCA

Variant names:

• chr13-48368533-AAC-A
• rs587778829
• NM_000321.3:c.1060_1061delCA

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.1060_1061delCA​(p.Gln354GlufsTer7) 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 (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RB1 NM_000321.3 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: 1.43

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 13-48368533-AAC-A is Pathogenic according to our data. Variant chr13-48368533-AAC-A is described in ClinVar as [Pathogenic]. Clinvar id is 126828.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-48368533-AAC-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RB1	NM_000321.3	c.1060_1061delCA	p.Gln354GlufsTer7	frameshift_variant	Exon 11 of 27	ENST00000267163.6	NP_000312.2
RB1	NM_001407165.1	c.1060_1061delCA	p.Gln354GlufsTer7	frameshift_variant	Exon 11 of 27		NP_001394094.1
RB1	NM_001407166.1	c.1060_1061delCA	p.Gln354GlufsTer7	frameshift_variant	Exon 11 of 17		NP_001394095.1
LOC112268118	XR_002957522.2	n.122-3559_122-3558delGT		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RB1	ENST00000267163.6	c.1060_1061delCA	p.Gln354GlufsTer7	frameshift_variant	Exon 11 of 27	1	NM_000321.3	ENSP00000267163.4
RB1	ENST00000650461.1	c.1060_1061delCA	p.Gln354GlufsTer7	frameshift_variant	Exon 11 of 27			ENSP00000497193.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: 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:1, TOTAL CASES:2, PEDIGREES:2. ACMG Codes Applied:PVS1, PM2 -

Feb 10, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Gln354Glufs*7) 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 been observed in individuals affected with retinoblastoma (PMID: 12541220, 15605413). This variant is also known as 1195delAC, g.65374_65375delCA in the literature. ClinVar contains an entry for this variant (Variation ID: 126828). Loss-of-function variants in RB1 are known to be pathogenic (PMID: 17096365). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Apr 07, 2015

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1060_1061delCA pathogenic mutation, located in coding exon 11 of the RB1 gene, results from a deletion of two nucleotides at positions 1060 and 1061, causing a translational frameshift with a predicted alternate stop codon. This mutation was previously identified in one study in one individual with retinoblastoma. Of note, this study refersto this alteration as 1195delAC(Richter S, Am. J. Hum. Genet. 2003 Feb; 72(2):253-69). In addition the clinical data presented in the literature, since frameshifts are typically deleterious in nature, this alteration is interpreted as a disease-causing mutation (ACMG Recommendations for Standards for Interpretation and Reporting of Sequence Variations. Revision 2007. Genet Med. 2008;10:294). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs587778829; hg19: chr13-48942669;