AMPD2 p.Arg106=
c.316C>A · VCV4789997
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, eas)
Conditions
2
pontocerebellar hypoplasia type 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.284 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.1 | GERP -3.2, phastCons 0.004 |
| Overall | ||
| CADD | 6.527 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
East Asian · 12/44,878 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.000929%
15/1,614,070 alleles · ultra-rare
exomes 13/1,461,732 · genomes 2/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0267% | 3,740 |
| Finnishnot grpmax-eligible | 0.00156% | 63,916 |
| African / African-American | 0.00133% | 75,060 |
| European (non-Finnish) | 8.47e-05% | 1,180,018 |
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.Arg106=
- Coding
- c.316C>A
- MANE Select
- NM_001368809
- Type
- single nucleotide variant
- Location
- chr1:109625755 (GRCh38)
- Gene constraint
- LOEUF 0.705 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 5 PDB
Similar variants
- AMPD2 p.Arg106Trp 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-arg106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown