COL2A1 p.Arg3fs
c.6dup · rs2540194271 · VCV2812872
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 haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 54 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.1, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- COL2A1
- Protein
- p.Arg3fs
- Coding
- c.6dup
- MANE Select
- NM_001844
- dbSNP
- rs2540194271
- Type
- Duplication
- Location
- chr12:48004315 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 11 PDB
Similar variants
- COL2A1 p.Arg3Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL2A1 p.Arg3Ser Uncertain significance ★ ⚠ same residue
- COL2A1 p.Arg3= Likely benign ★ same residue
- COL2A1 p.Arg3Leu Likely benign ★ same residue
- COL2A1 c.1680+2dup Pathogenic/Likely pathogenic ★★ same type
- COL2A1 c.1681-1dup Pathogenic ★★ same type
- COL2A1 c.2094_2094+1dup Pathogenic/Likely pathogenic ★★ same type
- COL2A1 p.Ala895fs Pathogenic ★★ 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/col2a1-p-arg3fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown