COL10A1 p.Pro358=
c.1074A>C · rs147229154 · VCV1630541
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
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 -0.12 | GERP -0.54, phastCons 0.73 |
| Overall | ||
| CADD | 3.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,950 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000342%
5/1,461,828 alleles · very rare
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
- COL10A1
- Protein
- p.Pro358=
- Coding
- c.1074A>C
- MANE Select
- NM_000493
- dbSNP
- rs147229154
- Type
- single nucleotide variant
- Location
- chr6:116121042 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 58.80 · 1 PDB
- Residue 358
- the 'disordered' region; the 'triple-helical region' region
Similar variants
- COL10A1 p.Pro358Leu Uncertain significance ★★ ⚠ same residue
- COL10A1 p.Arg71Ter Pathogenic/Likely pathogenic ★★ same type
- COL10A1 p.Cys591Arg Likely pathogenic ★★ same type
- COL10A1 p.Gln653Ter Pathogenic/Likely pathogenic ★★ same type
- COL10A1 p.Gly18Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- COL10A1 p.Gly18Glu Pathogenic/Likely pathogenic ★★ ⚠ same type
- COL10A1 p.Ser671Pro Pathogenic/Likely pathogenic ★★ same type
- COL10A1 p.Tyr597His 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/col10a1-p-pro358 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown