ERAP1 p.Asp406=
c.1218C>T · rs145458413 · VCV735010
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.88%, 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 1.1 | GERP -3, phastCons 0.027 |
| Overall | ||
| CADD | 3.406 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.88%
East Asian · 395/44,866 alleles
Filtering AF
0.809%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.781%
Overall
0.0501%
808/1,613,580 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.88% | 114 |
| Remaining individualsnot grpmax-eligible | 0.0736% | 1,359 |
| South Asian | 0.0494% | 2,024 |
| European (non-Finnish) | 0.0255% | 3,919 |
| African / African-American | 0.0187% | 5,357 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00833% | 12,004 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,590 |
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
- ERAP1
- Protein
- p.Asp406=
- Coding
- c.1218C>T
- MANE Select
- NM_001040458
- dbSNP
- rs145458413
- Type
- single nucleotide variant
- Location
- chr5:96792163 (GRCh38)
- Gene constraint
- LOEUF 0.947 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.78 · 27 PDB
- Residue 406
- a disulfide bond; an α-helix
Similar variants
- ERAP1 p.Asp406Asn Likely benign ★ same residue
- ERAP1 p.Ala356= Benign ★★ same type
- ERAP1 p.Gly514Arg Benign/Likely benign ★★ same type
- ERAP1 p.Ile915Thr Likely benign ★★ ⚠ same type
- ERAP1 p.Ser18= Benign/Likely benign ★★ same type
- ERAP1 p.Tyr57= Benign/Likely benign ★★ same type
- ERAP1 p.Tyr789= Benign ★★ same type
- ERAP2 p.Leu411Arg Benign/Likely benign ★★ ⚠ 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/erap1-p-asp406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown