AGMO p.Arg405Ter
c.1213C>T · rs139309795 · VCV501883
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 | escapes | premature termination codon within the last 50 nt of the penultimate exon (12 of 13, 50 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| REVEL | 0.01 | strongly benign-leaning |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.087 | GERP -5.1 |
| Overall | ||
| CADD | 35.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.528% | 189 |
| African / African-Americangrpmax | 0.179% | 559 |
| Remaining individualsnot grpmax-eligible | 0.0576% | 1,735 |
| Middle Eastern | 0.033% | 3,028 |
| Admixed American | 0.00834% | 11,985 |
| East Asian | 0.00446% | 22,415 |
| European (non-Finnish) | 0.00271% | 36,846 |
| South Asian | 0.0022% | 45,499 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- AGMO
- Protein
- p.Arg405Ter
- Coding
- c.1213C>T
- MANE Select
- NM_001004320
- dbSNP
- rs139309795
- Type
- single nucleotide variant
- Location
- chr7:15365564 (GRCh38)
- Gene constraint
- LOEUF 1.561 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.90
Similar variants
- AGMO p.Arg405Gln Likely benign ★★ same residue
- AGMO p.Arg405Leu Uncertain significance ★ ⚠ same residue
- AGMO p.Arg133Cys Uncertain significance ★★ ⚠ same type
- AGMO p.Arg83Gln Uncertain significance ★★ ⚠ same type
- AGMO p.Gly238Cys Uncertain significance ★★ ⚠ same type
- AGMO p.Gly322Ser Uncertain significance ★★ ⚠ same type
- AGMO p.Ile281Val Uncertain significance ★★ ⚠ same type
- AGMO p.Leu213Val 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/agmo-p-arg405ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown