PGAP2 p.Pro71Leu
c.212C>T · VCV3417284
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.157 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 0.94, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 14 kb · p 0.023 · regional, not allelic |
| Overall | ||
| CADD | 21.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PGAP2
- Protein
- p.Pro71Leu
- Coding
- c.212C>T
- MANE Select
- NM_014489
- Type
- single nucleotide variant
- Location
- chr11:3817399 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.00
Similar variants
- PGAP2 p.Ala187Thr Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Ala33Thr Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Arg238Cys Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Glu204Lys Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Leu161Phe Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Val183Met Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Val4Ile Uncertain significance ★★ ⚠ same condition
- PGAP2 p.Val182Ile Benign/Likely benign ★★ 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/pgap2-p-pro71leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown