Classification rationale

PVS1PM1PM2 Pathogenic

RB1 c.1027_1028del

NM_000321.2:c.1027_1028del (p.Leu343SerfsTer3) is a frameshift deletion in exon 10 of the RB1 gene, predicted to cause nonsense-mediated decay and complete loss of protein function. RB1 is a well-established tumor suppressor where loss of function is the accepted disease mechanism for retinoblastoma.¹ This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with a rare pathogenic variant not observed in the general population.² The frameshift at codon 343 removes the entire RB1 pocket domain, a critical functional domain for E2F binding and tumor suppressor activity.³ ClinVar classifies this variant as Pathogenic (Variation ID: 3236941, 1-star, single submitter). No variant-specific functional studies or clinical case reports were identified in the peer-reviewed literature.⁴

PVS1 + PM1 + PM2 → Pathogenic

1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment

2 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

3 pvs1_gene_context

4 clinvar ↗

Gene diagram · NM_000321.2 · variants mapped to exon structure

RB1 NM_000321.2

Fetching transcript structure from UCSC…

Applied criteria · 3 applied · 17 assessed

Applied · 3

Strength Supporting Moderate Strong Very strong

✓

PVS1 very strong Pathogenic

NM_000321.2:c.1027_1028del is a frameshift deletion in exon 10 of 27, predicted to introduce a premature termination codon at p.(Leu343SerfsTer3). NMD is expected as the stop codon occurs well before the last exon-exon junction. RB1 is a well-established tumor suppressor gene where loss of function is the accepted disease mechanism for retinoblastoma and associated cancers. Under ClinGen SVI PVS1 recommendations (PMC6185798), frameshift null variants in genes with established LOF mechanism are assigned PVS1 at very strong strength.

Frameshift variant in exon 10/27 introducing PTC at codon 345 (of 929)NMD expectedRB1 is a well-established tumor suppressor with LOF as disease mechanism

pvs1_generic_framework ↗

✓

PM1 moderate Pathogenic

This frameshift variant truncates the RB1 protein at p.Leu343, completely removing the pocket domain (spanning approximately residues 380-785), which is the critical functional domain responsible for E2F binding and tumor suppressor activity. The RB1 pocket domain is one of the most well-characterized functional domains in tumor biology. Although the variant is not located within a statistically significant hotspot at cancerhotspots.org, it removes a well-established critical functional domain, satisfying PM1 at moderate strength per domain-level application rules.

Frameshift at p.Leu343 removes the entire RB1 pocket domain (critical for E2F binding and tumor suppression)RB1 pocket domain is a well-characterized functional domain essential for tumor suppressor activity

✓

PM2 supporting Pathogenic

This variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), supporting a pathogenic role as a rare variant absent from the general population.

Absent from gnomAD v2.1 (population allele frequency 0.0%)Absent from gnomAD v4.1 (population allele frequency 0.0%)Absent from gnomAD-Canada v1.0

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

Assessed · not applied

Pathogenic

PS2 No de novo data available for this variant.

PS3 No functional studies directly testing NM_000321.2:c.1027_1028del were identified.

PS4 ClinVar submission SCV005046057 reports 2 cases (1 bilateral, 1 unilateral) from 1 pedigree, but this is a single submitter with no validated publication trail.

PM6 No de novo data available for this variant.

PP1 The ClinVar submission SCV005046057 extracted a PP1 signal (2 cases in 1 pedigree: 1 bilateral, 1 unilateral), but this is from a single submitter with no validated publication trail.

PP3 REVEL and BayesDel scores are not available for this variant as it is a deletion, not a single nucleotide variant.

PP4 Patient phenotype data is not available in the case materials.

PP5 This variant is classified as Pathogenic in ClinVar (Variation ID: 3236941) with review status 'criteria provided, single submitter' (1-star).

Benign

BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.

BS1 This variant is absent from all gnomAD populations.

BS2 No data available regarding observation of this variant in healthy adult controls.

BS3 No functional studies demonstrating a neutral or benign effect of this variant were identified.

BS4 No segregation data is available for this variant.

BP2 No data available regarding observation of this variant in trans with a known pathogenic variant.

BP4 REVEL and BayesDel are not available (not SNV).

BP5 No data available regarding observation of this variant in a case with an alternate molecular basis for disease.

BP6 ClinVar classifies this variant as Pathogenic, not Benign or Likely Benign.

N/A · 8 PS1 · PM3 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7

Research & evidence

Population frequency · supports pathogenic

gnomAD v4.1

gnomAD v2.1

v4.1

Absent from gnomAD v4.1.

v2.1

Absent from gnomAD v2.1.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v2.1

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory). (ClinVarID = 3236941)

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05).

SpliceAI ↗

Functional Likely Oncogenic

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

OncoKB ↗

COSMIC

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

This variant does not lie in a statistically significant hotspot. COSMIC could not be reviewed because the browser session was redirected to the login page before search results were available.

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Sources & reference links

8Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 9 PMIDs not cited in assessment

14769601 ↗ Rapid identification of germline mutations in retinoblastoma by protein truncation testing. ONCOKB

22205104 ↗ RB1 mutations and second primary malignancies after hereditary retinoblastoma. ONCOKB

26607597 ↗ Deletion of Rb1 induces both hyperproliferation and cell death in murine germinal center B cells. ONCOKB

30206110 ↗ The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial. ONCOKB

31138663 ↗ RB1 Deletion in Retinoblastoma Protein Pathway-Disrupted Cells Results in DNA Damage and Cancer Progression. ONCOKB

25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR

15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR

23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR

26140447 ↗ Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents. CLINVAR