AICDA p.Arg92Ter
c.274C>T · rs1227905250 · VCV804464
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
hyper-IgM syndrome type 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 0.79, phastCons 1 |
| Overall | ||
| CADD | 38.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AICDA
- Protein
- p.Arg92Ter
- Coding
- c.274C>T
- MANE Select
- NM_020661
- dbSNP
- rs1227905250
- Type
- single nucleotide variant
- Location
- chr12:8605368 (GRCh38)
- Gene constraint
- LOEUF 1.144 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.43 · 5 PDB
- Residue 92
- the cmp/dcmp-type deaminase domain; the 'required for interaction with rnf126' region; an α-helix
Similar variants
- AICDA p.Arg92= Likely benign ★ same residue
- AICDA p.Arg112Cys Pathogenic ★★ same condition
- AICDA p.Arg190Ter Pathogenic/Likely pathogenic ★★ same condition
- AICDA p.Arg24Trp Pathogenic ★★ same condition
- AICDA p.Arg99Ter Pathogenic/Likely pathogenic ★★ same condition
- AICDA p.Cys147Ter Pathogenic ★★ same condition
- AICDA p.Cys87Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
- AICDA p.Cys87Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/aicda-p-arg92ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown