RUNX2 p.Pro320fs
c.959del · VCV4819352
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
cleidocranial dysplasia 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- RUNX2
- Protein
- p.Pro320fs
- Coding
- c.959del
- MANE Select
- NM_001024630
- Type
- Deletion
- Location
- chr6:45512342 (GRCh38)
- Gene constraint
- LOEUF 0.352 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 59.02 · 4 PDB
- Residue 320
- a UniProt-annotated variant site (in clcd1; decreased subcellular localization in the nucleus; decreased transactivation activity); the 'disordered' region
Similar variants
- RUNX2 p.Pro320Leu Uncertain significance ★★ ⚠ same residue
- RUNX2 p.Asn120fs Likely pathogenic ★ same condition
- RUNX2 p.Cys350fs Likely pathogenic ★ same condition
- RUNX2 p.Gln209fs Likely pathogenic ★ same condition
- RUNX2 p.Gly462fs Pathogenic ★ same condition
- RUNX2 p.Leu136fs Pathogenic ★ same condition
- RUNX2 p.Phe187fs Likely pathogenic ★ same condition
- RUNX2 p.Phe376fs Likely pathogenic ★ same condition
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/runx2-p-pro320fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown