ECM1 p.Ala94=
c.282C>T · rs587692154 · VCV736513
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.079%, sas)
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 -0.24 | GERP -1.9 |
| Overall | ||
| CADD | 3.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.079%
South Asian · 72/91,084 alleles
Filtering AF
0.0643%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0589%
Overall
0.00458%
74/1,614,202 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.079% | 1,265 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
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
- ECM1
- Protein
- p.Ala94=
- Coding
- c.282C>T
- MANE Select
- NM_004425
- dbSNP
- rs587692154
- Type
- single nucleotide variant
- Location
- chr1:150509980 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.05
Similar variants
- ECM1 p.Arg254Ter Pathogenic ★★ same type
- ECM1 p.Arg416Ter Pathogenic/Likely pathogenic ★★ same type
- ECM1 p.Arg476Ter Pathogenic/Likely pathogenic ★★ same type
- ECM1 p.Arg53Ter Pathogenic ★★ same type
- ECM1 p.Cys269Tyr Pathogenic/Likely pathogenic ★★ same type
- ECM1 c.122-3T>G Uncertain significance ★★ same type
- ECM1 p.Arg185His Uncertain significance ★★ ⚠ same type
- ECM1 p.Asn324His 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/ecm1-p-ala94 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown