ELP2 p.Phe651=
c.1953C>T · rs200848954 · VCV791044
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.108%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.45 | GERP -4.7, phastCons 0.001 |
| Overall | ||
| CADD | 4.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.108%
Admixed American · 65/60,014 alleles
Filtering AF
0.0871%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0795%
Overall
0.00688%
111/1,613,864 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.108% | 923 |
| South Asian | 0.0286% | 3,502 |
| Middle Eastern | 0.0165% | 6,052 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| East Asian | 0.00446% | 22,422 |
| European (non-Finnish) | 0.00102% | 98,323 |
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.Phe651=
- Coding
- c.1953C>T
- MANE Select
- NM_018255
- dbSNP
- rs200848954
- Type
- single nucleotide variant
- Location
- chr18:36164666 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49 · 4 PDB
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-phe651 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown