ELP2 p.Lys591=
c.1773A>G · rs1598821004 · VCV735384
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -0.22, phastCons 1 |
| Overall | ||
| CADD | 13.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,934 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000186%
3/1,613,898 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,467 |
| European (non-Finnish) | 8.48e-05% | 1,179,883 |
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
- ELP2
- Protein
- p.Lys591=
- Coding
- c.1773A>G
- MANE Select
- NM_018255
- dbSNP
- rs1598821004
- Type
- single nucleotide variant
- Location
- chr18:36164486 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49 · 4 PDB
- Residue 591
- a turn
Similar variants
- ELP2 p.Arg140Ter Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.Arg462Gln Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.Gln192Ter Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.His206Arg Pathogenic/Likely pathogenic ★★ same type
- ELP2 c.523+574G>A Uncertain significance ★★ same type
- ELP2 p.Ala741Val Uncertain significance ★★ ⚠ same type
- ELP2 p.Arg468Trp Uncertain significance ★★ ⚠ same type
- ELP2 p.Asp71Gly Uncertain significance ★★ ⚠ same type
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/elp2-p-lys591 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown