Is RBP3 p.Ala873= (c.2619C>T) pathogenic?

RBP3 p.Ala873= (c.2619C>T) is classified Conflicting classifications of pathogenicity in RBP3 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-01-24). Rare (popmax 0.396%, mid); Associated with retinitis pigmentosa.

What condition is associated with RBP3 p.Ala873= (c.2619C>T)?

RBP3 p.Ala873= (c.2619C>T) is associated with retinitis pigmentosa (ClinVar).

How common is RBP3 p.Ala873= (c.2619C>T) in the general population?

RBP3 p.Ala873= (c.2619C>T) is rare (popmax 0.396%, mid) (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

RBP3 p.Ala873=

c.2619C>T · rs146045906 · VCV299960

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.396%, mid)

Conditions

retinitis pigmentosa

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 -20	GERP -3
Overall
CADD	0.023	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.396% Middle Eastern · 24/6,060 alleles

Filtering AF 0.273% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.232%

Overall 0.142% 2,286/1,612,664 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.396%	252
European (non-Finnish)	0.182%	551
Remaining individualsnot grpmax-eligible	0.0736%	1,359
African / African-American	0.044%	2,275
Admixed American	0.0383%	2,610
Finnishnot grpmax-eligible	0.0176%	5,684
East Asian	0.00446%	22,439
South Asian	0.00439%	22,767
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,598

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.Ala873=
Coding: c.2619C>T
MANE Select: NM_005225 · reported on NM_002900
dbSNP: rs146045906
Type: single nucleotide variant
Location: chr10:47351103 (GRCh38)
Structure: AlphaFold pLDDT 63.40 · 8 PDB

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

Disease context

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

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

RBP3 p.Ala873Thr Uncertain significance ★ ⚠ same residue
RBP3 p.Ala263Ser Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala312Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala379Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala403Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala688Val Uncertain significance ★★ ⚠ same condition
RBP3 p.Ala803Thr Uncertain significance ★★ ⚠ same condition
RBP3 p.Arg170Gln 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-ala873 (accessed [today's date]).

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