APRT p.Leu162del
c.484_486del · rs2142950877 · VCV1367702
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
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 1.9 | GERP -1.5, phastCons 0.034 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- APRT
- Protein
- p.Leu162del
- Coding
- c.484_486del
- MANE Select
- NM_000485
- dbSNP
- rs2142950877
- Type
- Deletion
- Location
- chr16:88809755 (GRCh38)
- Gene constraint
- LOEUF 1.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.91 · 16 PDB
- Residue 162
- an α-helix
Similar variants
- APRT p.Thr96fs Pathogenic/Likely pathogenic ★★ same type
- APRT c.401-40_401-25del Likely pathogenic ★ same type
- APRT p.Ala37fs Pathogenic ★ same type
- APRT p.Glu158del Pathogenic ★ same type
- APRT p.Glu5fs Likely pathogenic ★ same type
- APRT p.Gly94fs Pathogenic ★ same type
- APRT p.Leu130fs Pathogenic ★ same type
- APRT p.Leu85fs 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-leu162del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown