Is EYS p.Arg794Ter (c.2380C>T) pathogenic?

EYS p.Arg794Ter (c.2380C>T) is classified Pathogenic in EYS (ClinVar, Multiple submitters, 11 submitters; last evaluated 2025-03-27). Very rare (popmax 0.00245%, eas); Associated with inherited retinal dystrophy.

What condition is associated with EYS p.Arg794Ter (c.2380C>T)?

EYS p.Arg794Ter (c.2380C>T) is associated with inherited retinal dystrophy, retinitis pigmentosa 25, retinitis pigmentosa (ClinVar).

How common is EYS p.Arg794Ter (c.2380C>T) in the general population?

EYS p.Arg794Ter (c.2380C>T) is very rare (popmax 0.00245%, eas) (gnomAD).

EYS p.Arg794Ter

c.2380C>T · rs371032798 · VCV650440

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00245%, eas)

Conditions

inherited retinal dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 15 of 43
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.3	GERP 0.023
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00245% East Asian · 1/40,740 alleles

Filtering AF 0.000559% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000441%

Overall 0.000904% 14/1,548,716 alleles · very rare exomes 14/1,396,576 · genomes 0/152,140 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00245%	40,740
Remaining individualsnot grpmax-eligible	0.00167%	59,944
European (non-Finnish)	0.00105%	95,430

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.Arg794Ter
Coding: c.2380C>T
MANE Select: NM_001142800
dbSNP: rs371032798
Type: single nucleotide variant
Location: chr6:64945794 (GRCh38)
Gene constraint: LOEUF 0.96 · pLI <0.01 (gnomAD)
Residue 794: the egf-like 10; calcium-binding domain

Full EYS 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

Also linked: retinitis pigmentosa 25 retinitis pigmentosa

Similar variants

EYS p.Arg794Gln Uncertain significance ★★ ⚠ same residue
EYS p.Arg794fs Likely pathogenic ★ 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

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-arg794ter (accessed [today's date]).

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