ECEL1 p.Thr248=
c.744G>C · rs201178152 · VCV785995
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.384%, afr)
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 -14 | GERP -2.7 |
| Overall | ||
| CADD | 0.132 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.384%
African / African-American · 285/74,184 alleles
Filtering AF
0.347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.333%
Overall
0.0208%
327/1,572,492 alleles · rare
exomes 137/1,420,122 · genomes 190/152,370 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.384% | 260 |
| Admixed American | 0.0331% | 3,023 |
| Remaining individualsnot grpmax-eligible | 0.023% | 4,357 |
| South Asian | 0.00347% | 28,846 |
| European (non-Finnish) | 0.000603% | 165,935 |
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
- ECEL1
- Protein
- p.Thr248=
- Coding
- c.744G>C
- MANE Select
- NM_004826
- dbSNP
- rs201178152
- Type
- single nucleotide variant
- Location
- chr2:232485910 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62
- Residue 248
- the peptidase m13 domain
Similar variants
- ECEL1 c.1685+1G>A Pathogenic ★★ same type
- ECEL1 c.2151+2T>C Likely pathogenic ★★ same type
- ECEL1 c.966+1G>A Pathogenic ★★ same type
- ECEL1 p.Ala675Thr Pathogenic ★★ same type
- ECEL1 p.Arg333Ter Pathogenic ★★ same type
- ECEL1 p.Arg395Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- ECEL1 p.Arg418Cys Likely pathogenic ★★ same type
- ECEL1 p.Gln435Ter 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/ecel1-p-thr248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown