Is EYS p.Ser595fs (c.1784_1787del) pathogenic?

EYS p.Ser595fs (c.17841787del) is classified Likely pathogenic in EYS (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-09). No gnomAD frequency available for this variant; Associated with EYS-related disorder.

What condition is associated with EYS p.Ser595fs (c.1784_1787del)?

EYS p.Ser595fs (c.1784_1787del) is associated with EYS-related disorder (ClinVar).

How common is EYS p.Ser595fs (c.1784_1787del) in the general population?

EYS p.Ser595fs (c.1784_1787del) is no gnomAD frequency available for this variant (gnomAD).

EYS p.Ser595fs

c.1784_1787del · rs1768657480 · VCV867151

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

EYS-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 12 of 43
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.22	GERP -0.17
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EYS
Protein: p.Ser595fs
Coding: c.1784_1787del
MANE Select: NM_001142800
dbSNP: rs1768657480
Type: Deletion
Location: chr6:65296099 (GRCh38)
Gene constraint: LOEUF 0.96 · pLI <0.01 (gnomAD)
Residue 595: the egf-like 6 domain

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

Disease context

EYS-related disorder

Similar variants

EYS p.Ala2957fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Asn1773_Val1781delinsLys Pathogenic/Likely pathogenic ★★ same condition
EYS p.Asn2918fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Asn328fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Cys412fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Cys78fs Pathogenic ★★ same condition
EYS p.Gln2723fs Pathogenic/Likely pathogenic ★★ same condition
EYS p.Gln3053fs 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-p-ser595fs (accessed [today's date]).

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