AICDA p.Arg25=
c.75T>C · rs1028378638 · VCV1940023
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
Conditions
1
hyper-IgM syndrome type 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.17 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4 | GERP -3.7 |
| Overall | ||
| CADD | 1.195 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,086 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000821%
12/1,461,728 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,362 |
| European (non-Finnish) | 0.000763% | 131,104 |
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
- AICDA
- Protein
- p.Arg25=
- Coding
- c.75T>C
- MANE Select
- NM_020661
- dbSNP
- rs1028378638
- Type
- single nucleotide variant
- Location
- chr12:8606946 (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 25
- the cmp/dcmp-type deaminase domain; a UniProt-annotated variant site (in); the 'interaction with supt6h' region
Similar variants
- AICDA p.Arg25Cys Uncertain significance ★★ ⚠ same residue
- AICDA p.Arg25His Benign/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.Arg92Ter Pathogenic/Likely pathogenic ★★ same condition
- AICDA p.Arg99Ter Pathogenic/Likely pathogenic ★★ same condition
- AICDA p.Cys147Ter 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-arg25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown