IRF2BPL p.Ser134=
c.402C>T · rs764059898 · VCV2644406
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00598%, nfe)
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 0.083, phastCons 1 |
| Overall | ||
| CADD | 11.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00598%
European (non-Finnish) · 67/1,120,166 alleles
Filtering AF
0.00478%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00439%
Overall
0.00457%
68/1,486,786 alleles · very rare
exomes 66/1,348,632 · genomes 2/138,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00598% | 16,719 |
| Remaining individualsnot grpmax-eligible | 0.00175% | 57,302 |
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.Ser134=
- Coding
- c.402C>T
- MANE Select
- NM_024496
- dbSNP
- rs764059898
- Type
- single nucleotide variant
- Location
- chr14:77027391 (GRCh38)
- Gene constraint
- LOEUF 0.544 · pLI 0.91 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.01 · 1 PDB
- Residue 134
- a UniProt-annotated variant site (in nedamss); a UniProt-annotated variant site (in nedamss; loss of function)
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-ser134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown