AMPD3 p.Ala21=
c.63G>A · rs142453229 · VCV3050911
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.18%, afr)
Conditions
1
AMPD3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.8 |
| Overall | ||
| CADD | 0.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.18%
African / African-American · 135/75,050 alleles
Filtering AF
0.155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.146%
Overall
0.011%
177/1,614,224 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.18% | 556 |
| Admixed American | 0.0416% | 2,401 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000424% | 236,008 |
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
- AMPD3
- Protein
- p.Ala21=
- Coding
- c.63G>A
- MANE Select
- NM_001025389
- dbSNP
- rs142453229
- Type
- single nucleotide variant
- Location
- chr11:10461582 (GRCh38)
- Gene constraint
- LOEUF 0.817 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.74
Disease context
AMPD3-related disorder
Similar variants
- AMPD3 c.1135-6C>A Likely benign same condition
- AMPD3 c.1431-3C>T Likely benign same condition
- AMPD3 c.1431-7C>A Likely benign same condition
- AMPD3 c.-6+944G>T Likely benign same condition
- AMPD3 p.Asn292= Likely benign same condition
- AMPD3 p.Asp478= Likely benign same condition
- AMPD3 p.Gln434= Likely benign same condition
- AMPD3 p.Thr272= Likely benign 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/ampd3-p-ala21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown