AMPD2 p.Asp285del
c.852CGA[1] · rs1650781134 · VCV956565
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000341%, nfe)
Conditions
2
pontocerebellar hypoplasia type 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -0.12, phastCons 0.018 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000341%
European (non-Finnish) · 4/1,173,318 alleles
Filtering AF
8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000275%
4/1,451,958 alleles · very rare
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.Asp285del
- Coding
- c.852CGA[1]
- MANE Select
- NM_001368809
- dbSNP
- rs1650781134
- Type
- Microsatellite
- Location
- chr1:109627308 (GRCh38)
- Gene constraint
- LOEUF 0.705 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 5 PDB
Similar variants
- AMPD2 p.Asp285= Benign/Likely benign ★★ same residue
- AMPD2 p.Asp285Asn Uncertain significance ★ ⚠ same residue
- AMPD2 p.Glu725del Uncertain significance ★★ same condition
- 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
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-asp285del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown