Is RBP3 p.Ser137= (c.411C>T) pathogenic?

RBP3 p.Ser137= (c.411C>T) is classified Likely benign in RBP3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-11-27). Ultra-rare (popmax 0.0602%, eas); Associated with inherited retinal dystrophy.

What condition is associated with RBP3 p.Ser137= (c.411C>T)?

RBP3 p.Ser137= (c.411C>T) is associated with inherited retinal dystrophy (ClinVar).

How common is RBP3 p.Ser137= (c.411C>T) in the general population?

RBP3 p.Ser137= (c.411C>T) is ultra-rare (popmax 0.0602%, eas) (gnomAD).

RBP3 p.Ser137=

c.411C>T · rs184452710 · VCV761157

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0602%, 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 0.24	GERP 1.6, phastCons 0.28
Overall
CADD	5.694	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0602% East Asian · 27/44,874 alleles

Filtering AF 0.0424% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0365%

Overall 0.00322% 52/1,613,784 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0602%	1,662
Remaining individualsnot grpmax-eligible	0.0144%	6,944
African / African-American	0.00267%	37,516
South Asian	0.0022%	45,542
Admixed American	0.00167%	60,036
European (non-Finnish)	0.000932%	107,272

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.Ser137=
Coding: c.411C>T
MANE Select: NM_005225 · reported on NM_002900
dbSNP: rs184452710
Type: single nucleotide variant
Location: chr10:47348895 (GRCh38)
Structure: AlphaFold pLDDT 63.40 · 8 PDB
Residue 137: a DNA-binding region; the 'interaction with birc2/c-iap1' 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.Ser137Gly 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-ser137 (accessed [today's date]).

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