AMPD2 p.Thr401=
c.1203G>A · rs756936910 · VCV707757
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
Conditions
2
pontocerebellar hypoplasia type 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.033 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -3.9 |
| Overall | ||
| CADD | 7.413 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/60,010 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00229%
37/1,613,924 alleles · very rare
exomes 34/1,461,746 · genomes 3/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 12,002 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| European (non-Finnish) | 0.00246% | 40,691 |
| East Asian | 0.00223% | 44,886 |
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
- AMPD2
- Protein
- p.Thr401=
- Coding
- c.1203G>A
- MANE Select
- NM_001368809
- dbSNP
- rs756936910
- Type
- single nucleotide variant
- Location
- chr1:109628205 (GRCh38)
- Gene constraint
- LOEUF 0.705 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 5 PDB
- Residue 401
- a β-strand
Similar variants
- AMPD2 p.Thr401Met Uncertain significance ★★ same residue
- AMPD2 c.1698+1G>A Pathogenic/Likely pathogenic ★★ same condition
- AMPD2 p.Arg353Ter Pathogenic/Likely pathogenic ★★ same condition
- AMPD2 p.Arg449Ter Pathogenic/Likely pathogenic ★★ same condition
- AMPD2 p.Arg620His Pathogenic/Likely pathogenic ★★ same condition
- AMPD2 p.Arg789His Likely pathogenic ★★ same condition
- AMPD2 p.Glu174Ter Pathogenic/Likely pathogenic ★★ same condition
- AMPD2 c.1080+3G>A Uncertain significance ★★ 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/ampd2-p-thr401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown