Is RP2 p.Pro202= (c.606T>C) pathogenic?

RP2 p.Pro202= (c.606T>C) is classified Benign/Likely benign in RP2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-04). Low-frequency (popmax 1.26%, afr); Associated with retinitis pigmentosa.

What condition is associated with RP2 p.Pro202= (c.606T>C)?

RP2 p.Pro202= (c.606T>C) is associated with retinitis pigmentosa (ClinVar).

How common is RP2 p.Pro202= (c.606T>C) in the general population?

RP2 p.Pro202= (c.606T>C) is low-frequency (popmax 1.26%, afr) (gnomAD).

How is Retinitis pigmentosa inherited?

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

RP2 p.Pro202=

c.606T>C · rs144795993 · VCV788051

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.26%, afr)

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 0.98	GERP 0.52, phastCons 0.78
Overall
CADD	8.443	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.26% African / African-American · 720/57,289 alleles

Filtering AF 1.18% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.15%

Overall 0.0676% 818/1,210,135 alleles · low-frequency exomes 399/1,098,142 · genomes 419/111,993 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.26%	80
Admixed American	0.103%	972
Remaining individualsnot grpmax-eligible	0.0924%	1,082
Middle Eastern	0.0689%	1,452
South Asian	0.00176%	56,806
European (non-Finnish)	0.000335%	298,416

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: RP2
Protein: p.Pro202=
Coding: c.606T>C
MANE Select: NM_006915
dbSNP: rs144795993
Type: single nucleotide variant
Location: chrX:46853979 (GRCh38)
Structure: AlphaFold pLDDT 91.64 · 3 PDB
Residue 202: an α-helix

Full RP2 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

RP2 p.Arg118Cys Pathogenic/Likely pathogenic ★★ same condition
RP2 p.Arg120Ter Pathogenic ★★ same condition
RP2 p.Cys122Tyr Pathogenic/Likely pathogenic ★★ same condition
RP2 p.Leu253Arg Likely pathogenic ★★ same condition
RP2 c.*33C>G Uncertain significance ★★ same condition
RP2 p.Arg282Gln Uncertain significance ★★ ⚠ same condition
RP2 p.Ile166Val Uncertain significance ★★ ⚠ same condition
RP2 p.Ser172Gly 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/rp2-p-pro202 (accessed [today's date]).

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