EDC3 p.Ser507=
c.1521T>C · rs184299954 · VCV756592
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.108%, amr)
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 -0.51 | GERP -3.8 |
| Overall | ||
| CADD | 7.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.108%
Admixed American · 65/60,032 alleles
Filtering AF
0.0871%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0795%
Overall
0.00533%
86/1,613,482 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.108% | 924 |
| Middle Eastern | 0.0352% | 2,843 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,804 |
| European (non-Finnish) | 0.000509% | 196,639 |
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.Ser507=
- Coding
- c.1521T>C
- MANE Select
- NM_025083
- dbSNP
- rs184299954
- Type
- single nucleotide variant
- Location
- chr15:74632618 (GRCh38)
- Gene constraint
- LOEUF 0.656 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 77.04 · 6 PDB
Similar variants
- EDC3 p.Arg260Trp Uncertain significance ★★ ⚠ same type
- EDC3 p.Thr273= Benign ★★ 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-ser507 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown