ELN p.Lys463=
c.1389A>G · rs2486128144 · VCV3052790
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ELN-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.005 | GERP 1.7, phastCons 0.038 |
| Overall | ||
| CADD | 3.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ELN
- Protein
- p.Lys463=
- Coding
- c.1389A>G
- MANE Select
- NM_000501
- dbSNP
- rs2486128144
- Type
- single nucleotide variant
- Location
- chr7:74057671 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 36.20
Disease context
ELN-related disorder
Similar variants
- ELN p.Lys463Arg Benign/Likely benign ★★ same residue
- ELN c.800-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ELN p.Arg541Ter Pathogenic ★★ same condition
- ELN p.Gln442Ter Pathogenic ★★ same condition
- ELN p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
- ELN p.Ala447Thr Uncertain significance ★★ ⚠ same condition
- ELN p.Ala637Ser Uncertain significance ★★ ⚠ same condition
- ELN p.Gly398Arg 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/eln-p-lys463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown