IRF2BPL p.Asp552=
c.1656C>T · rs1227932885 · VCV2578722
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00527%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 0.044, phastCons 1 |
| Overall | ||
| CADD | 8.109 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00527%
European (non-Finnish) · 61/1,157,548 alleles
Filtering AF
0.00418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00379%
Overall
0.00399%
62/1,552,960 alleles · very rare
exomes 60/1,400,896 · genomes 2/152,064 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00527% | 18,976 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,188 |
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
- IRF2BPL
- Protein
- p.Asp552=
- Coding
- c.1656C>T
- MANE Select
- NM_024496
- dbSNP
- rs1227932885
- Type
- single nucleotide variant
- Location
- chr14:77026137 (GRCh38)
- Gene constraint
- LOEUF 0.544 · pLI 0.91 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.01 · 1 PDB
- Residue 552
- a UniProt-annotated variant site (in nedamss); a UniProt-annotated variant site (in nedamss; loss of function); the 'disordered' region
Similar variants
- IRF2BPL p.Arg188Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln117Ter Likely pathogenic ★★ same type
- IRF2BPL p.Gln119Ter Likely pathogenic ★★ same type
- IRF2BPL p.Gln120Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln121Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln122Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln167Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln497Ter Pathogenic/Likely pathogenic ★★ 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/irf2bpl-p-asp552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown