Is RB1 p.Cys489= (c.1467C>T) pathogenic?

RB1 p.Cys489= (c.1467C>T) is classified Benign/Likely benign in RB1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-06-24). Ultra-rare (popmax 0.0271%, afr); Associated with retinoblastoma.

What condition is associated with RB1 p.Cys489= (c.1467C>T)?

RB1 p.Cys489= (c.1467C>T) is associated with retinoblastoma, hereditary neoplastic syndrome (ClinVar).

How common is RB1 p.Cys489= (c.1467C>T) in the general population?

RB1 p.Cys489= (c.1467C>T) is ultra-rare (popmax 0.0271%, afr) (gnomAD).

How is Retinoblastoma inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

RB1 p.Cys489=

c.1467C>T · rs141608408 · VCV416486

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0271%, afr)

Conditions

retinoblastoma

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.53	GERP -3.4, phastCons 0.085
Overall
CADD	8.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0271% African / African-American · 20/73,926 alleles

Filtering AF 0.0179% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0149%

Overall 0.00268% 43/1,603,876 alleles · ultra-rare exomes 35/1,454,112 · genomes 8/149,764 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0271%	3,696
South Asian	0.00222%	44,998
Admixed American	0.00168%	59,542
European (non-Finnish)	0.00162%	61,837
Remaining individualsnot grpmax-eligible	0.00161%	62,068

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: RB1
Protein: p.Cys489=
Coding: c.1467C>T
MANE Select: NM_000321
dbSNP: rs141608408
Type: single nucleotide variant
Location: chr13:48380210 (GRCh38)
Gene constraint: LOEUF 0.239 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.03 · 19 PDB
Residue 489: an α-helix; the 'pocket; binds t and e1a' region; the 'domain a' region

Full RB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinoblastoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

For Retinoblastoma (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Antenatal, Childhood, Infancy
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

RB1 p.Cys489Gly Uncertain significance ★★ ⚠ same residue
RB1 p.Cys489Trp Uncertain significance ★★ ⚠ same residue
RB1 p.Cys489Arg Uncertain significance ★ ⚠ same residue
RB1 p.Cys489Tyr Conflicting classifications of pathogenicity ★ ⚠ same residue
RB1 c.1049+1G>A Pathogenic/Likely pathogenic ★★ same condition
RB1 c.1049+1G>T Pathogenic/Likely pathogenic ★★ same condition
RB1 c.1049+3A>G Pathogenic/Likely pathogenic ★★ same condition
RB1 c.1050-2A>G Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rb1-p-cys489 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown