Is RBP3 p.Arg86= (c.258C>T) pathogenic?

RBP3 p.Arg86= (c.258C>T) is classified Conflicting classifications of pathogenicity in RBP3 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2023-06-13). Very rare (popmax 0.00254%, nfe); Associated with retinitis pigmentosa.

What condition is associated with RBP3 p.Arg86= (c.258C>T)?

RBP3 p.Arg86= (c.258C>T) is associated with retinitis pigmentosa (ClinVar).

How common is RBP3 p.Arg86= (c.258C>T) in the general population?

RBP3 p.Arg86= (c.258C>T) is very rare (popmax 0.00254%, nfe) (gnomAD).

How is Retinitis pigmentosa inherited?

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

RBP3 p.Arg86=

c.258C>T · rs376194840 · VCV299996

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00254%, nfe)

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 -0.53	GERP -3.3
Overall
CADD	6.474	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00254% European (non-Finnish) · 30/1,180,034 alleles

Filtering AF 0.0018% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00156%

Overall 0.00192% 31/1,613,498 alleles · very rare exomes 26/1,461,318 · genomes 5/152,180 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00254%	39,334
African / African-American	0.00133%	74,922

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.Arg86=
Coding: c.258C>T
MANE Select: NM_002900
dbSNP: rs376194840
Type: single nucleotide variant
Location: chr10:47348742 (GRCh38)
Structure: AlphaFold pLDDT 63.40 · 8 PDB
Residue 86: 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

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.Arg86Cys Uncertain significance ★★ ⚠ same residue
RBP3 p.Arg86His 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

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-arg86 (accessed [today's date]).

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