MMP2 p.Ser647=
c.1941C>T · rs112831239 · VCV749065
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0253%, afr)
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 -8.2 | GERP -4.6 |
| Overall | ||
| CADD | 2.342 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0253%
African / African-American · 19/75,030 alleles
Filtering AF
0.0165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.0039%
63/1,614,096 alleles · ultra-rare
exomes 50/1,461,874 · genomes 13/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0253% | 3,949 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| East Asian | 0.00446% | 22,429 |
| European (non-Finnish) | 0.00246% | 40,690 |
| Admixed American | 0.00167% | 60,014 |
| South Asian | 0.0011% | 91,076 |
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.Ser647=
- Coding
- c.1941C>T
- MANE Select
- NM_004530
- dbSNP
- rs112831239
- Type
- single nucleotide variant
- Location
- chr16:55505400 (GRCh38)
- Gene constraint
- LOEUF 0.654 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.31 · 14 PDB
- Residue 647
- the 'required for inhibitor timp2 binding' region; a β-strand
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-ser647 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown