AMPD1 c.34+3G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
myopathy due to myoadenylate deaminase deficiency
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.43 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.77 | GERP 1.3, phastCons 1 |
| Non-coding constraint | Z -1.98 | 1 kb window · o/e 1.16 · regional · uncalibrated |
| Overall | ||
| CADD | 21.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,970 alleles
Overall
0.000657%
1/152,136 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
- AMPD1
- Coding
- c.34+3G>A
- MANE Select
- NM_000036
- dbSNP
- rs557611277
- Type
- single nucleotide variant
- Location
- chr1:114693433 (GRCh38)
- Gene constraint
- LOEUF 1.036 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.84
Similar variants
- AMPD1 p.Gln653Ter Pathogenic/Likely pathogenic ★★ same condition
- AMPD1 c.1388+5G>A Uncertain significance ★★ same condition
- AMPD1 c.1974+1G>A Uncertain significance ★★ same condition
- AMPD1 c.-42C>T Uncertain significance ★★ ⚠ same condition
- AMPD1 p.Ala308Thr Uncertain significance ★★ ⚠ same condition
- AMPD1 p.Ala489Thr Uncertain significance ★★ ⚠ same condition
- AMPD1 p.Ala578Thr Uncertain significance ★★ ⚠ same condition
- AMPD1 p.Ala616Thr 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/ampd1-c-34-plus-3g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown