COL2A1 p.Pro893fs
c.2678del · rs1938958532 · VCV1455693
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 40 of 54 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.062 | GERP -0.41, phastCons 0.53 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No allele count reported in gnomAD v4.1 (AN 1,554,086). 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.Pro893fs
- Coding
- c.2678del
- MANE Select
- NM_001844
- dbSNP
- rs1938958532
- Type
- Deletion
- Location
- chr12:47980010 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 11 PDB
- Residue 893
- the 'disordered' region; the 'triple-helical region' region
Disease context
Similar variants
- COL2A1 c.1023+3_1023+6del Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 c.906_924+9del Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 p.Asp1234fs Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 p.Gly1047fs Pathogenic ★★ same condition
- COL2A1 p.Gly1119fs Pathogenic ★★ same condition
- COL2A1 p.Gly165fs Pathogenic ★★ same condition
- COL2A1 p.Gly171fs Pathogenic ★★ same condition
- COL2A1 p.Gly831fs Pathogenic/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/col2a1-p-pro893fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown