EDC3 p.Thr273=
c.819G>A · rs76943949 · VCV712171
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.56%, 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 -8.9 | GERP -4.5 |
| Overall | ||
| CADD | 0.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.56%
African / African-American · 1,164/74,734 alleles
Filtering AF
1.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.45%
Overall
0.0913%
1,463/1,601,976 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.56% | 64 |
| Remaining individualsnot grpmax-eligible | 0.137% | 728 |
| South Asian | 0.113% | 888 |
| Admixed American | 0.111% | 901 |
| Middle Eastern | 0.017% | 5,870 |
| European (non-Finnish) | 0.00384% | 26,019 |
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
- EDC3
- Protein
- p.Thr273=
- Coding
- c.819G>A
- MANE Select
- NM_025083
- dbSNP
- rs76943949
- Type
- single nucleotide variant
- Location
- chr15:74655734 (GRCh38)
- Gene constraint
- LOEUF 0.656 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 77.04 · 6 PDB
- Residue 273
- the 'required for interaction with ddx6' region
Similar variants
- EDC3 p.Thr273Met Uncertain significance ★ ⚠ same residue
- EDC3 p.Arg260Trp Uncertain significance ★★ ⚠ same type
- EDC3 c.821-2A>C Uncertain significance ★ same type
- EDC3 p.Ala129Thr Uncertain significance ★ ⚠ same type
- EDC3 p.Ala172Pro Uncertain significance ★ ⚠ same type
- EDC3 p.Ala312Thr Uncertain significance ★ ⚠ same type
- EDC3 p.Arg232His Uncertain significance ★ ⚠ same type
- EDC3 p.Arg243Gln 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/edc3-p-thr273 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown