Is EYS p.Arg431Ser (c.1293A>T) pathogenic?

EYS p.Arg431Ser (c.1293A>T) is classified Uncertain significance in EYS (ClinVar, Multiple submitters, 6 submitters; last evaluated 2024-01-11). AlphaMissense: likely benign (0.2694); Ultra-rare (popmax 0.0166%, mid); Associated with retinitis pigmentosa 25.

What condition is associated with EYS p.Arg431Ser (c.1293A>T)?

EYS p.Arg431Ser (c.1293A>T) is associated with retinitis pigmentosa 25, retinitis pigmentosa (ClinVar).

How common is EYS p.Arg431Ser (c.1293A>T) in the general population?

EYS p.Arg431Ser (c.1293A>T) is ultra-rare (popmax 0.0166%, mid) (gnomAD).

How is Retinitis pigmentosa inherited?

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

What do computational predictors say about EYS p.Arg431Ser (c.1293A>T)?

AlphaMissense predicts likely benign (score 0.2694) — an in-silico prediction, not a clinical call.

EYS p.Arg431Ser

c.1293A>T · rs371607669 · VCV912059

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.2694 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0166%, mid)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

retinitis pigmentosa 25

Computational evidence

Protein change
AlphaMissense	0.2694	likely benign
REVEL	0.162	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP 1.8, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 1,775 kb · p 4.6e-07 · regional, not allelic
Overall
CADD	17.85	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0166% Middle Eastern · 1/6,012 alleles

Filtering AF 0.00592% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00545%

Overall 0.00632% 100/1,583,022 alleles · ultra-rare exomes 94/1,431,122 · genomes 6/151,900 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0166%	6,012
Remaining individualsnot grpmax-eligible	0.0147%	6,824
Admixed American	0.0101%	9,943
European (non-Finnish)	0.00719%	13,908
African / African-American	0.00135%	74,250

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: EYS
Protein: p.Arg431Ser
Coding: c.1293A>T
MANE Select: NM_001142800
dbSNP: rs371607669
Type: single nucleotide variant
Location: chr6:65384392 (GRCh38)
Gene constraint: LOEUF 0.96 · pLI <0.01 (gnomAD)

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

Disease context

retinitis pigmentosa 25 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa

For Retinitis pigmentosa (Orphanet):

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

Similar variants

EYS p.Arg431= Likely benign ★ same residue
EYS c.1056+1G>A Pathogenic/Likely pathogenic ★★ same condition
EYS c.1056+3A>C Likely pathogenic ★★ same condition
EYS c.1057-1G>A Likely pathogenic ★★ same condition
EYS c.1184+1G>A Pathogenic/Likely pathogenic ★★ same condition
EYS c.1184+1G>T Likely pathogenic ★★ same condition
EYS c.1185-1G>A Likely pathogenic ★★ same condition
EYS c.1299+2T>A Likely pathogenic ★★ 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/eys-p-arg431ser (accessed [today's date]).

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