APRT p.Val125=
c.375C>T · rs763991694 · VCV1896491
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, 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 -4 | GERP -3.3 |
| Overall | ||
| CADD | 0.235 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
African / African-American · 5/74,918 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00211%
34/1,613,116 alleles · very rare
exomes 31/1,460,902 · genomes 3/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00667% | 14,984 |
| South Asian | 0.00329% | 30,361 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,236 |
| European (non-Finnish) | 0.00203% | 49,167 |
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.Val125=
- Coding
- c.375C>T
- MANE Select
- NM_000485
- dbSNP
- rs763991694
- Type
- single nucleotide variant
- Location
- chr16:88810095 (GRCh38)
- Gene constraint
- LOEUF 1.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.91 · 16 PDB
- Residue 125
- a β-strand
Similar variants
- APRT p.Val125Ile Uncertain significance ★ ⚠ same residue
- 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
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-val125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown