COL11A1 p.Lys43=
c.129A>G · rs1408601971 · VCV2841998
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.2 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000342%
5/1,460,934 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,058 |
| European (non-Finnish) | 0.000339% | 294,879 |
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
- COL11A1
- Protein
- p.Lys43=
- Coding
- c.129A>G
- MANE Select
- NM_001854
- dbSNP
- rs1408601971
- Type
- single nucleotide variant
- Location
- chr1:103082950 (GRCh38)
- Gene constraint
- LOEUF 0.349 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 53.06
Similar variants
- COL11A1 p.Lys43Gln Uncertain significance ★ ⚠ same residue
- COL11A1 c.1245+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL11A1 c.1245+1G>T Pathogenic/Likely pathogenic ★★ same type
- COL11A1 c.1629+1G>A Likely pathogenic ★★ same type
- COL11A1 c.1630-1G>T Pathogenic ★★ same type
- COL11A1 c.1791+1G>T Likely pathogenic ★★ same type
- COL11A1 c.1900-1G>A Likely pathogenic ★★ same type
- COL11A1 c.2241+5G>T Pathogenic/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/col11a1-p-lys43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown