ELP2 p.Thr58=
c.174C>T · rs150889303 · VCV3035545
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0527%, sas)
Conditions
1
ELP2-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 -0.077 | GERP -4.2, phastCons 0.11 |
| Overall | ||
| CADD | 10.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0527%
South Asian · 48/91,066 alleles
Filtering AF
0.0408%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0366%
Overall
0.00496%
80/1,613,716 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0527% | 1,897 |
| Middle Eastern | 0.0329% | 3,041 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,238 |
| African / African-American | 0.00267% | 37,444 |
| European (non-Finnish) | 0.00212% | 47,192 |
| Admixed American | 0.00167% | 59,994 |
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.Thr58=
- Coding
- c.174C>T
- MANE Select
- NM_018255
- dbSNP
- rs150889303
- Type
- single nucleotide variant
- Location
- chr18:36133273 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.49 · 4 PDB
Disease context
ELP2-related disorder
Similar variants
- ELP2 c.523+574G>A Uncertain significance ★★ same condition
- ELP2 p.Phe658Leu Uncertain significance ★★ ⚠ same condition
- ELP2 p.Ile356Met Uncertain significance ★ ⚠ same condition
- ELP2 p.Cys231Tyr Likely benign ⚠ same condition
- ELP2 p.Tyr345= Likely benign same condition
- ELP2 p.Arg140Ter Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.Arg462Gln Pathogenic/Likely pathogenic ★★ same type
- ELP2 p.Gln192Ter Pathogenic/Likely pathogenic ★★ 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-thr58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown