ELP1 p.Ser596fs
c.1787_1788del · VCV4759288
Likely pathogenic
Multiple submitters
Classification
Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Riley-Day syndrome
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 16 of 37 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.23 | GERP 1.7 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ELP1
- Protein
- p.Ser596fs
- Coding
- c.1787_1788del
- MANE Select
- NM_003640
- Type
- Microsatellite
- Location
- chr9:108902905 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.31 · 5 PDB
Disease context
Riley-Day syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Familial dysautonomia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
- Prevalence
- <1 / 1 000 000 (Europe)
Similar variants
- ELP1 p.Ser596Pro Uncertain significance ★ ⚠ same residue
- ELP1 c.1751_1752del Pathogenic/Likely pathogenic ★★ same condition
- ELP1 p.Asp539fs Pathogenic/Likely pathogenic ★★ same condition
- ELP1 p.Asp775fs Pathogenic/Likely pathogenic ★★ same condition
- ELP1 p.Cys84fs Pathogenic/Likely pathogenic ★★ same condition
- ELP1 p.Tyr1278fs Pathogenic/Likely pathogenic ★★ same condition
- ELP1 p.Val408fs Likely pathogenic ★★ same condition
- ELP1 p.Ser536del Uncertain significance ★★ 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/elp1-p-ser596fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown