Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.84%, afr)
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 -0.21 | GERP -0.015, phastCons 0.22 |
| Overall | ||
| CADD | 5.886 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.84%
African / African-American · 2,854/74,416 alleles
Filtering AF
3.72%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.67%
Overall
0.205%
3,272/1,594,510 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.84% | 26 |
| Admixed American | 0.306% | 327 |
| Remaining individualsnot grpmax-eligible | 0.278% | 360 |
| Middle Eastern | 0.255% | 392 |
| South Asian | 0.0113% | 8,842 |
| European (non-Finnish) | 0.00376% | 26,611 |
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
- APRT
- Protein
- p.Ser30=
- Coding
- c.90G>T
- MANE Select
- NM_000485
- dbSNP
- rs8191472
- Type
- single nucleotide variant
- Location
- chr16:88811647 (GRCh38)
- Gene constraint
- LOEUF 1.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.91 · 16 PDB
- Residue 30
- an α-helix; a modified residue (phosphoserine)
Similar variants
- APRT p.Arg67Gln Likely pathogenic ★★ same type
- APRT p.Arg67Ter Pathogenic ★★ same type
- APRT p.Arg87Ter Pathogenic ★★ same type
- APRT p.Asp65Val Pathogenic ★★ same type
- APRT p.Gly133Arg Likely pathogenic ★★ same type
- APRT p.Gly63Asp Likely pathogenic ★★ same type
- APRT p.Met1Ile Pathogenic ★★ same type
- APRT p.Met1Val Pathogenic ★★ same type
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/aprt-p-ser30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown