Is EYS c.749del pathogenic?

EYS c.749del is classified Pathogenic/Likely pathogenic in EYS (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-20). Very rare (popmax 0.000597%, nfe); Associated with retinitis pigmentosa 25.

What condition is associated with EYS c.749del?

EYS c.749del is associated with retinitis pigmentosa 25 (ClinVar).

How common is EYS c.749del in the general population?

EYS c.749del is very rare (popmax 0.000597%, nfe) (gnomAD).

How is Retinitis pigmentosa inherited?

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

EYS c.749del

rs762794153 · VCV1417445

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000597%, nfe)

Conditions

retinitis pigmentosa 25

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.1	GERP -2.9
Non-coding constraint	Z -2.55	1 kb window · o/e 1.20 · regional · uncalibrated

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000597% European (non-Finnish) · 7/1,173,468 alleles

Filtering AF 0.000248% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00016%

Overall 0.000436% 7/1,606,378 alleles · very rare exomes 7/1,454,120 · genomes 0/152,258 · joint denominator

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
Coding: c.749del
MANE Select: NM_001142800
dbSNP: rs762794153
Type: Deletion
Location: chr6:65490707 (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

For Retinitis pigmentosa (Orphanet):

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

Similar variants

EYS c.1057del Pathogenic/Likely pathogenic ★★ same condition
EYS c.5928-3_5928-1del Pathogenic/Likely pathogenic ★★ same condition
EYS c.5928del Pathogenic ★★ same condition
EYS c.6079-3_6079-2del Pathogenic/Likely pathogenic ★★ same condition
EYS p.Ala1520fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Ala1557fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Ala2957fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Ala3058_Tyr3059insTer Pathogenic/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-c-749del (accessed [today's date]).

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