PGAP2 p.Leu14=
c.42G>C · VCV3702173
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 9.513 | 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.Leu14=
- Coding
- c.42G>C
- MANE Select
- NM_014489
- Type
- single nucleotide variant
- Location
- chr11:3811301 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.00
Similar variants
- PGAP2 p.Ala127Val Likely pathogenic ★★ same type
- PGAP2 p.Arg238Pro Pathogenic/Likely pathogenic ★★ ⚠ same type
- PGAP2 p.Thr294Met Likely pathogenic ★★ same type
- PGAP2 c.602-3C>T Uncertain significance ★★ same type
- PGAP2 p.Ala187Thr Uncertain significance ★★ ⚠ same type
- PGAP2 p.Ala33Thr Uncertain significance ★★ ⚠ same type
- PGAP2 p.Arg238Cys Uncertain significance ★★ ⚠ same type
- PGAP2 p.Asn205Lys Uncertain significance ★★ ⚠ 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/pgap2-p-leu14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown