Is EYS p.Cys866= (c.2598C>T) pathogenic?

EYS p.Cys866= (c.2598C>T) is classified Conflicting classifications of pathogenicity in EYS (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-18). Rare (popmax 0.126%, amr); Associated with retinitis pigmentosa.

What condition is associated with EYS p.Cys866= (c.2598C>T)?

EYS p.Cys866= (c.2598C>T) is associated with retinitis pigmentosa (ClinVar).

How common is EYS p.Cys866= (c.2598C>T) in the general population?

EYS p.Cys866= (c.2598C>T) is rare (popmax 0.126%, amr) (gnomAD).

How is Retinitis pigmentosa inherited?

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

EYS p.Cys866=

c.2598C>T · rs183814213 · VCV710846

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.126%, amr)

Conditions

retinitis pigmentosa

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.1	phastCons 0.29
Overall
CADD	4.654	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.126% Admixed American · 64/50,984 alleles

Filtering AF 0.101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0919%

Overall 0.0438% 680/1,551,212 alleles · rare exomes 620/1,399,030 · genomes 60/152,182 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.126%	797
European (non-Finnish)	0.0492%	2,033
Remaining individualsnot grpmax-eligible	0.0483%	2,072
Ashkenazi Jewishnot grpmax-eligible	0.0454%	2,204
Middle Eastern	0.0167%	5,990
African / African-American	0.00957%	10,447
Finnishnot grpmax-eligible	0.00334%	29,938

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.Cys866=
Coding: c.2598C>T
MANE Select: NM_001142800
dbSNP: rs183814213
Type: single nucleotide variant
Location: chr6:64912527 (GRCh38)
Gene constraint: LOEUF 0.96 · pLI <0.01 (gnomAD)
Residue 866: the egf-like 12 domain; a disulfide bond

Full EYS 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

EYS p.Cys866Arg Uncertain significance ★★ ⚠ same residue
EYS c.1056+1G>A Pathogenic/Likely pathogenic ★★ same condition
EYS c.1766+1G>T Pathogenic/Likely pathogenic ★★ same condition
EYS c.2259+1G>A Pathogenic/Likely pathogenic ★★ same condition
EYS c.3164+1G>A Pathogenic/Likely pathogenic ★★ same condition
EYS c.3243+1G>A Pathogenic/Likely pathogenic ★★ same condition
EYS c.3443+1G>T Pathogenic/Likely pathogenic ★★ same condition
EYS c.5928-2A>G 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-cys866 (accessed [today's date]).

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