Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 42.6%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.68 | GERP -1.8 |
| Overall | ||
| CADD | 0.492 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
42.6%
African / African-American · 26,683/62,596 alleles
Filtering AF
42.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 42%
Overall
9.58%
95,439/996,258 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 42.6% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 17.7% | 6 |
| Middle Eastern | 14% | 7 |
| South Asian | 12.4% | 8 |
| Remaining individualsnot grpmax-eligible | 10.7% | 9 |
| Admixed American | 7.87% | 13 |
| European (non-Finnish) | 6.66% | 15 |
| Amishnot grpmax-eligible | 4.39% | 23 |
| Finnishnot grpmax-eligible | 3.84% | 26 |
| East Asian | 1.89% | 53 |
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
- Coding
- c.*178A>G
- MANE Select
- NM_000485
- dbSNP
- rs4695
- Type
- single nucleotide variant
- Location
- chr16:88809520 (GRCh38)
- Gene constraint
- LOEUF 1.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.91 · 16 PDB
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-c-star-178a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown