# NM_002427.4(MMP13):c.1101C>G (p.Pro367=)

https://sugi.bio/variant/mmp13-p-pro367

## Summary

**MMP13 p.Pro367= (c.1101C>G)** is classified **Conflicting classifications of pathogenicity** in MMP13 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-10-17). Very rare (popmax 0.00136%, nfe); Associated with metaphyseal anadysplasia.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs781949882 · 2 submitters · 2 linked conditions · very rare (popmax 0.00136%, nfe)

## For patients & families {#patients}

This is a change in the MMP13 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 2 submitters, and is linked to metaphyseal anadysplasia.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant, Autosomal recessive |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | MMP13 is a diagnostic-grade gene on 4 Genomics England panels |

**Commonly reported features of Metaphyseal anadysplasia** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Abnormal metaphysis morphology — Very frequent (99-80%)
- Joint stiffness — Very frequent (99-80%)
- Abnormality of the lower limb — Very frequent (99-80%)
- Abnormality of ulnar metaphysis — Very frequent (99-80%)
- Short stature — Very frequent (99-80%)
- Abnormality of epiphysis morphology — Very frequent (99-80%)
- Bowing of the long bones — Very frequent (99-80%)
- Aplasia/Hypoplasia of the radius — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0003562/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [MMP13](https://sugi.bio/atlas/gene/MMP13/) |
| Protein change (HGVS p.) | p.Pro367= |
| Coding change (HGVS c.) | c.1101C>G |
| MANE Select transcript | [NM_002427](https://www.ncbi.nlm.nih.gov/nuccore/NM_002427) |
| dbSNP | [rs781949882](https://www.ncbi.nlm.nih.gov/snp/rs781949882/) |
| Variant type | single nucleotide variant |
| Location | chr11:102948001-102948001 (GRCh38) |
| ClinVar | [VCV717251](https://www.ncbi.nlm.nih.gov/clinvar/variation/717251/) |

**All HGVS expressions:** `NC_000011.10:g.102948001G>C`, `NC_000011.9:g.102818730G>C`, `NG_021404.1:g.12734C>G`, `NM_002427.4:c.1101C>G`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 0.058, GERP -2.23, phastCons 0.498 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 5.447**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00136%** (nfe) · FAF95 0.000803% · FAF99 0.00065% · 16/1,179,812 in the highest group · 16/1,613,422 alleles overall — very rare (popmax 0.00136%, nfe).

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**MMP13** population constraint: LOEUF 1.067, pLI 1.2947e-10, missense-Z 0.58112. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **367** lies in a disulfide bond; the 'interaction with collagen' region; a β-strand.

AlphaFold model confidence (whole protein): pLDDT 89.00, 75% of residues very-high.

**49 experimental structure(s)** (PDB): [1EUB](https://www.rcsb.org/structure/1EUB), [1FLS](https://www.rcsb.org/structure/1FLS), [1FM1](https://www.rcsb.org/structure/1FM1), [1PEX](https://www.rcsb.org/structure/1PEX), [1XUC](https://www.rcsb.org/structure/1XUC), [1XUD](https://www.rcsb.org/structure/1XUD).

## What this gene does {#gene-function}

*Describes the biological roles of MMP13 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** MMP13's established molecular role includes endopeptidase activity. p.Pro367= falls in the interaction with collagen region.


### Pathways affected {#pathways}

MMP13 participates in **5 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Activation of Matrix Metalloproteinases](https://reactome.org/content/detail/R-HSA-1592389) | curated |
| [Assembly of collagen fibrils and other multimeric structures](https://reactome.org/content/detail/R-HSA-2022090) | curated |
| [RUNX2 regulates genes involved in cell migration](https://reactome.org/content/detail/R-HSA-8941332) | curated |
| [Collagen degradation](https://reactome.org/content/detail/R-HSA-1442490) | electronic |
| [Degradation of the extracellular matrix](https://reactome.org/content/detail/R-HSA-1474228) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** endopeptidase activity, metalloendopeptidase activity, calcium ion binding, collagen binding, zinc ion binding.

**Biological process:** extracellular matrix disassembly, collagen catabolic process, bone morphogenesis.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2022-10-17.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Likely benign).

**Submission history:** 3 submissions (2018–2022); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-15 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-10-17 |

## Associated conditions {#conditions}

[metaphyseal anadysplasia](https://sugi.bio/atlas/disease/metaphyseal-anadysplasia/), [spondyloepimetaphyseal dysplasia, Missouri type](https://sugi.bio/atlas/disease/spondyloepimetaphyseal-dysplasia-missouri-type/).

**Reported phenotype names (ClinVar):** Metaphyseal anadysplasia, not provided, Spondyloepimetaphyseal dysplasia, Missouri type, none provided, Early-onset regressive form of metaphyseal dysplasia.

## Similar variants {#similar}

Related MMP13 variant pages (same residue, condition, or type): [MMP13 p.Pro367Leu](/variant/mmp13-p-pro367leu), [MMP13 p.Arg333Cys](/variant/mmp13-p-arg333cys), [MMP13 p.Gly237Glu](/variant/mmp13-p-gly237glu), [MMP13 p.Leu218Val](/variant/mmp13-p-leu218val), [MMP13 p.Pro273Arg](/variant/mmp13-p-pro273arg), [MMP13 c.799+7C>T](/variant/mmp13-c-799-plus-7c-t), [MMP13 c.799+8G>A](/variant/mmp13-c-799-plus-8g-a), [MMP13 c.800-9C>T](/variant/mmp13-c-800-minus-9c-t).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 717251). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*