Is RBP3 p.Ser80= (c.240C>T) pathogenic?

RBP3 p.Ser80= (c.240C>T) is classified Uncertain significance in RBP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-01). Very rare (popmax 0.00223%, eas); Associated with inherited retinal dystrophy.

What condition is associated with RBP3 p.Ser80= (c.240C>T)?

RBP3 p.Ser80= (c.240C>T) is associated with inherited retinal dystrophy (ClinVar).

How common is RBP3 p.Ser80= (c.240C>T) in the general population?

RBP3 p.Ser80= (c.240C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

RBP3 p.Ser80=

c.240C>T · rs2549027476 · VCV3028179

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

inherited retinal dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.13	GERP -1.7, phastCons 0.65
Overall
CADD	6.388	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,882 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000274% 4/1,461,290 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,882
European (non-Finnish)	0.000254%	393,343

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: RBP3
Protein: p.Ser80=
Coding: c.240C>T
MANE Select: NM_005225 · reported on NM_002900
dbSNP: rs2549027476
Type: single nucleotide variant
Location: chr10:47348724 (GRCh38)
Structure: AlphaFold pLDDT 63.40 · 8 PDB
Residue 80: the 'disordered' region; the 'cyclin a:cdk2 binding' region

Full RBP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

inherited retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RBP3 p.Ser80Arg Uncertain significance ★ same residue
RBP3 p.Gln141Ter Pathogenic/Likely pathogenic ★★ same condition
RBP3 p.Glu149Ter Pathogenic ★★ same condition
RBP3 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala325Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala546Val Uncertain significance ★★ same condition
RBP3 p.Ala570Val Uncertain significance ★★ same condition
RBP3 p.Ala803Thr Uncertain significance ★★ ⚠ 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/rbp3-p-ser80 (accessed [today's date]).

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