COL11A1 p.Ser170=
c.510C>T · rs749497678 · VCV501234
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, afr)
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 -2.3 | GERP -3.5 |
| Overall | ||
| CADD | 8.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,810 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.00273%
44/1,612,960 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,312 |
| European (non-Finnish) | 0.00297% | 33,701 |
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.Ser170=
- Coding
- c.510C>T
- MANE Select
- NM_001854
- dbSNP
- rs749497678
- Type
- single nucleotide variant
- Location
- chr1:103074759 (GRCh38)
- Gene constraint
- LOEUF 0.349 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 53.06
- Residue 170
- the laminin g-like domain; a disulfide bond
Similar variants
- COL11A1 p.Ser170Arg 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-ser170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown