Is ELN p.Lys594fs (c.1779del) pathogenic?

ELN p.Lys594fs (c.1779del) is classified Likely pathogenic in ELN (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-20). Associated with cutis laxa, autosomal dominant 1.

What condition is associated with ELN p.Lys594fs (c.1779del)?

ELN p.Lys594fs (c.1779del) is associated with cutis laxa, autosomal dominant 1 (ClinVar).

How is Autosomal dominant cutis laxa inherited?

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

ELN p.Lys594fs

c.1779del · VCV3775199

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

cutis laxa, autosomal dominant 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 26 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.5	GERP 6.4, phastCons 1

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

Variant & gene context

Gene: ELN
Protein: p.Lys594fs
Coding: c.1779del
MANE Select: NM_000501
Type: Deletion
Location: chr7:74061131 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.20

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

Disease context

cutis laxa, autosomal dominant 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant cutis laxa (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal

Similar variants

ELN p.Ala718fs Likely pathogenic ★★ same condition
ELN p.Gly688fs Pathogenic ★★ same condition
ELN p.Leu56fs Pathogenic/Likely pathogenic ★★ same condition
ELN p.Gly653fs Likely pathogenic ★ same condition
ELN p.Pro658fs Pathogenic ★ same condition
ELN p.479VAPGVG[1] Conflicting classifications of pathogenicity ★ same condition
ELN p.Arg721fs Likely pathogenic same condition
ELN p.Gly649fs 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/eln-p-lys594fs (accessed [today's date]).

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