AMPD3 p.Gln434=
c.1302G>A · rs376077336 · VCV3034967
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0666%, nfe)
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 5.1 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.665 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0666%
European (non-Finnish) · 786/1,180,036 alleles
Filtering AF
0.0627%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0612%
Overall
0.05%
806/1,613,474 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0666% | 1,501 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,459 |
| African / African-American | 0.00801% | 12,485 |
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.Gln434=
- Coding
- c.1302G>A
- MANE Select
- NM_001025389
- dbSNP
- rs376077336
- Type
- single nucleotide variant
- Location
- chr11:10495605 (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.Ala21= Likely benign same condition
- AMPD3 p.Asn292= Likely benign same condition
- AMPD3 p.Asp478= 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-gln434 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown