PYCR2 p.Ala27=
c.81T>A · VCV4764776
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 | 0.036 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.04 | GERP -3.4, phastCons 0.03 |
| Overall | ||
| CADD | 10.01 | 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
- PYCR2
- Protein
- p.Ala27=
- Coding
- c.81T>A
- MANE Select
- NM_013328
- Type
- single nucleotide variant
- Location
- chr1:225923758 (GRCh38)
- Gene constraint
- LOEUF 1.029 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.60 · 2 PDB
- Residue 27
- a β-strand
Similar variants
- PYCR2 p.Arg119Cys Pathogenic/Likely pathogenic ★★ same type
- PYCR2 p.Arg119His Likely pathogenic ★★ same type
- PYCR2 p.Arg266Ter Pathogenic ★★ same type
- PYCR2 p.Gln226Ter Pathogenic/Likely pathogenic ★★ same type
- PYCR2 p.Ala187Thr Uncertain significance ★★ ⚠ same type
- PYCR2 p.Arg17Pro Uncertain significance ★★ ⚠ same type
- PYCR2 p.Arg200Cys Uncertain significance ★★ ⚠ same type
- PYCR2 p.Ile82Thr 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/pycr2-p-ala27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown