EDC4 p.Thr911=
c.2733C>G · rs138068113 · VCV2646643
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.66%, mid)
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 0.27 | GERP 0.53, phastCons 0.98 |
| Overall | ||
| CADD | 6.052 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.66%
Middle Eastern · 40/6,062 alleles
Filtering AF
0.498%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.442%
Overall
0.317%
5,124/1,614,114 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.66% | 152 |
| European (non-Finnish) | 0.37% | 270 |
| Remaining individualsnot grpmax-eligible | 0.342% | 292 |
| Ashkenazi Jewishnot grpmax-eligible | 0.334% | 299 |
| Finnishnot grpmax-eligible | 0.262% | 381 |
| Admixed American | 0.213% | 469 |
| African / African-American | 0.0813% | 1,230 |
| South Asian | 0.0472% | 2,118 |
| East Asian | 0.00223% | 44,882 |
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
- EDC4
- Protein
- p.Thr911=
- Coding
- c.2733C>G
- MANE Select
- NM_014329
- dbSNP
- rs138068113
- Type
- single nucleotide variant
- Location
- chr16:67881361 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.59 (gnomAD)
- Structure
- AlphaFold pLDDT 63.18
- Residue 911
- the 'disordered' region
Similar variants
- EDC4 p.Gly309= Benign ★★ same type
- EDC4 p.Ala1030Val Uncertain significance ★ ⚠ same type
- EDC4 p.Ala1036Thr Uncertain significance ★ ⚠ same type
- EDC4 p.Ala1076Thr Uncertain significance ★ ⚠ same type
- EDC4 p.Ala1117Asp Uncertain significance ★ ⚠ same type
- EDC4 p.Ala1284Val Uncertain significance ★ ⚠ same type
- EDC4 p.Ala26Gly Uncertain significance ★ ⚠ same type
- EDC4 p.Ala315Val 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/edc4-p-thr911 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown