ERAP1 p.Tyr789=
c.2367T>C · rs142985224 · VCV714090
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.06%, sas)
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 2.6 | GERP -0.69, phastCons 1 |
| Overall | ||
| CADD | 6.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.06%
South Asian · 970/91,084 alleles
Filtering AF
1.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.987%
Overall
0.102%
1,643/1,614,192 alleles · low-frequency
exomes 1,546/1,461,876 · genomes 97/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.06% | 94 |
| Middle Eastern | 0.495% | 202 |
| Remaining individualsnot grpmax-eligible | 0.118% | 845 |
| Admixed American | 0.107% | 938 |
| European (non-Finnish) | 0.042% | 2,379 |
| African / African-American | 0.00666% | 15,009 |
| East Asian | 0.00446% | 22,437 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Finnishnot grpmax-eligible | 0.00156% | 64,030 |
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.Tyr789=
- Coding
- c.2367T>C
- MANE Select
- NM_001040458
- dbSNP
- rs142985224
- Type
- single nucleotide variant
- Location
- chr5:96781773 (GRCh38)
- Gene constraint
- LOEUF 0.947 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.78 · 27 PDB
- Residue 789
- an α-helix
Similar variants
- ERAP2 p.Asp789Asn Uncertain significance ★ ⚠ same residue
- ERAP2 p.Asp789Val Uncertain significance ★ 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
- 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-tyr789 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown