COL1A2 p.Gln1237Ter
c.3709C>T · VCV4896868
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 50 of 52 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 48.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- COL1A2
- Protein
- p.Gln1237Ter
- Coding
- c.3709C>T
- MANE Select
- NM_000089
- Type
- single nucleotide variant
- Location
- chr7:94428475 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.02 · 5 PDB
- Residue 1237
- the fibrillar collagen nc1 domain; a disulfide bond
Similar variants
- COL1A2 p.Gln1237Arg Uncertain significance ★★ ⚠ same residue
- COL1A2 c.1197+5G>A Pathogenic ★★ same type
- COL1A2 c.1404+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL1A2 c.1503+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL1A2 c.1503+1G>C Pathogenic ★★ same type
- COL1A2 c.1557+3A>G Pathogenic ★★ same type
- COL1A2 c.1971+1G>A Pathogenic ★★ same type
- COL1A2 c.1972-1G>T Likely 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/col1a2-p-gln1237ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown