MMP2 p.His403=
c.1209C>T · rs200422763 · VCV1386502
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.2 | GERP -4.5 |
| Overall | ||
| CADD | 0.573 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,088 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.0139%
224/1,614,092 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,073 |
| Middle Eastern | 0.0164% | 6,084 |
| European (non-Finnish) | 0.0164% | 6,114 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,811 |
| Admixed American | 0.005% | 20,004 |
| East Asian | 0.00446% | 22,441 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
| African / African-American | 0.00133% | 74,928 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MMP2
- Protein
- p.His403=
- Coding
- c.1209C>T
- MANE Select
- NM_004530
- dbSNP
- rs200422763
- Type
- single nucleotide variant
- Location
- chr16:55491829 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.31 · 14 PDB
- Residue 403
- an α-helix; the 'collagenase-like 2' region; a binding site
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-his403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown