APRT p.Phe174del
c.518TCT[1] · rs121912681 · VCV18294
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, afr)
Conditions
2
APRT-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 16.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/75,052 alleles
Filtering AF
0.00814%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00632%
Overall
0.00632%
102/1,613,428 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0147% | 6,823 |
| East Asian | 0.0134% | 7,482 |
| European (non-Finnish) | 0.00644% | 15,526 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,625 |
| Finnishnot grpmax-eligible | 0.00316% | 31,641 |
| South Asian | 0.0022% | 45,544 |
| Admixed American | 0.00167% | 60,030 |
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.Phe174del
- Coding
- c.518TCT[1]
- MANE Select
- NM_000485
- dbSNP
- rs121912681
- Type
- Microsatellite
- Location
- chr16:88809718 (GRCh38)
- Gene constraint
- LOEUF 1.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.91 · 16 PDB
- Residue 174
- a β-strand
Similar variants
- APRT p.Leu97fs Pathogenic ★★ same condition
- APRT p.Arg67Gln Likely pathogenic ★★ same condition
- APRT p.Arg67Ter Pathogenic ★★ same condition
- APRT p.Arg87Ter Pathogenic ★★ same condition
- APRT p.Asp65Val Pathogenic ★★ same condition
- APRT p.Gly133Arg Likely pathogenic ★★ same condition
- APRT p.Gly63Asp Likely pathogenic ★★ same condition
- APRT p.Met1Ile Pathogenic ★★ 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/aprt-p-phe174del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown