COL11A2 p.Arg48=
c.144G>A · rs373983197 · VCV1200328
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00246%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.72 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -3.4, phastCons 0.88 |
| Overall | ||
| CADD | 8.833 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00246%
European (non-Finnish) · 29/1,180,032 alleles
Filtering AF
0.00172%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00149%
Overall
0.00186%
30/1,613,034 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00246% | 40,691 |
| Admixed American | 0.00167% | 60,008 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- COL11A2
- Protein
- p.Arg48=
- Coding
- c.144G>A
- MANE Select
- NM_080680
- dbSNP
- rs373983197
- Type
- single nucleotide variant
- Location
- chr6:33189408 (GRCh38)
- Gene constraint
- LOEUF 0.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.18
Similar variants
- COL11A2 p.Arg48Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL11A2 p.Arg48Leu Uncertain significance ★ ⚠ same residue
- COL11A2 p.Arg48Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL11A2 c.1119+1G>A Likely pathogenic ★★ same type
- COL11A2 c.1819-2A>G Likely pathogenic ★★ same type
- COL11A2 c.3852+1G>T Likely pathogenic ★★ same type
- COL11A2 c.4392+1G>A Pathogenic ★★ same type
- COL11A2 c.607-2A>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/col11a2-p-arg48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown