EDEM2 p.Arg424=
c.1272C>T · rs527248500 · VCV737798
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.145%, eas)
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 2.7 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 10.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.145%
East Asian · 65/44,884 alleles
Filtering AF
0.117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.106%
Overall
0.00483%
78/1,614,168 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.145% | 691 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| South Asian | 0.00549% | 18,216 |
| African / African-American | 0.00133% | 75,052 |
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
- EDEM2
- Protein
- p.Arg424=
- Coding
- c.1272C>T
- MANE Select
- NM_018217
- dbSNP
- rs527248500
- Type
- single nucleotide variant
- Location
- chr20:35115898 (GRCh38)
- Gene constraint
- LOEUF 0.749 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.61
Similar variants
- EDEM2 p.Arg424Cys Uncertain significance ★ ⚠ same residue
- EDEM2 p.Arg424His Uncertain significance ⚠ same residue
- EDEM2 p.Ala251Thr Uncertain significance ★ ⚠ same type
- EDEM2 p.Ala484Thr Uncertain significance ★ ⚠ same type
- EDEM2 p.Ala529Glu Uncertain significance ★ ⚠ same type
- EDEM2 p.Ala81Thr Uncertain significance ★ same type
- EDEM2 p.Arg219Thr Uncertain significance ★ ⚠ same type
- EDEM2 p.Arg224Cys 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/edem2-p-arg424 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown