MMP14 p.Asn439=
c.1317C>T · rs779771554 · VCV1901555
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 -10 | GERP -5 |
| Overall | ||
| CADD | 2.107 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,880 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00124%
20/1,613,540 alleles · very rare
exomes 16/1,461,412 · genomes 4/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,960 |
| African / African-American | 0.00401% | 24,967 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,460 |
| South Asian | 0.0011% | 91,008 |
| European (non-Finnish) | 0.00102% | 98,315 |
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
- MMP14
- Protein
- p.Asn439=
- Coding
- c.1317C>T
- MANE Select
- NM_004995
- dbSNP
- rs779771554
- Type
- single nucleotide variant
- Location
- chr14:22845266 (GRCh38)
- Gene constraint
- LOEUF 0.312 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.66 · 12 PDB
- Residue 439
- a β-strand
Similar variants
- MMP14 p.Asn439Thr Uncertain significance ★★ ⚠ same residue
- MMP14 c.850+2C>T Uncertain significance ★★ same type
- MMP14 p.Ala165Asp Uncertain significance ★★ ⚠ same type
- MMP14 p.Ala366Val Uncertain significance ★★ ⚠ same type
- MMP14 p.Ala539Thr Uncertain significance ★★ ⚠ same type
- MMP14 p.Ala539Val Uncertain significance ★★ ⚠ same type
- MMP14 p.Arg168Cys Uncertain significance ★★ ⚠ same type
- MMP14 p.Arg343Trp 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/mmp14-p-asn439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown