MMP2 p.Pro563=
c.1689T>C · VCV4716529
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. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -5.5 |
| Overall | ||
| CADD | 10.42 | 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
- MMP2
- Protein
- p.Pro563=
- Coding
- c.1689T>C
- MANE Select
- NM_004530
- Type
- single nucleotide variant
- Location
- chr16:55498368 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.31 · 14 PDB
- Residue 563
- a turn; the 'required for inhibitor timp2 binding' region
Similar variants
- MMP2 p.Cys102Ter Pathogenic/Likely pathogenic ★★ same type
- MMP2 p.Ser396Arg Pathogenic/Likely pathogenic ★★ same type
- MMP2 p.Tyr244Ter Pathogenic ★★ same type
- MMP2 c.380+6G>A Uncertain significance ★★ same type
- MMP2 p.Ala42Ser Uncertain significance ★★ ⚠ same type
- MMP2 p.Ala545Val Uncertain significance ★★ ⚠ same type
- MMP2 p.Arg115Leu Uncertain significance ★★ same type
- MMP2 p.Arg296His 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/mmp2-p-pro563 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown