IRAK2 p.Asp202=
c.606C>T · rs56154338 · VCV2653516
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.478%, 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 -20 | GERP -3.6 |
| Overall | ||
| CADD | 0.084 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.478%
Middle Eastern · 29/6,062 alleles
Filtering AF
0.413%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.409%
Overall
0.347%
5,605/1,614,126 alleles · rare
exomes 5,249/1,461,862 · genomes 356/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.478% | 209 |
| European (non-Finnish) | 0.423% | 237 |
| Remaining individualsnot grpmax-eligible | 0.301% | 332 |
| South Asian | 0.208% | 482 |
| Admixed American | 0.113% | 883 |
| Finnishnot grpmax-eligible | 0.106% | 942 |
| African / African-American | 0.0733% | 1,364 |
| East Asian | 0.0357% | 2,804 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,869 |
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
- IRAK2
- Protein
- p.Asp202=
- Coding
- c.606C>T
- MANE Select
- NM_001570
- dbSNP
- rs56154338
- Type
- single nucleotide variant
- Location
- chr3:10213284 (GRCh38)
- Gene constraint
- LOEUF 0.962 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.76 · 1 PDB
Similar variants
- IRAK2 p.Asp202Val Uncertain significance ★ ⚠ same residue
- IRAK2 p.Leu392Val Benign ★★ same type
- IRAK2 p.Ala152Thr Uncertain significance ★ ⚠ same type
- IRAK2 p.Ala192Thr Uncertain significance ★ ⚠ same type
- IRAK2 p.Ala451Ser Uncertain significance ★ ⚠ same type
- IRAK2 p.Ala477Thr Uncertain significance ★ ⚠ same type
- IRAK2 p.Ala573Ser Uncertain significance ★ ⚠ same type
- IRAK2 p.Ala601Val 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/irak2-p-asp202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown