COL20A1 p.Pro175=
c.525C>T · rs771551505 · VCV2652520
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0494%, mid)
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>A here scores Δ0.43 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -2.2 |
| Overall | ||
| CADD | 2.475 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0494%
Middle Eastern · 3/6,070 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.00688%
111/1,612,258 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0494% | 2,023 |
| South Asian | 0.0274% | 3,643 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,919 |
| Admixed American | 0.00834% | 11,997 |
| European (non-Finnish) | 0.00568% | 17,607 |
| African / African-American | 0.00267% | 37,463 |
| East Asian | 0.00223% | 44,896 |
| Finnishnot grpmax-eligible | 0.00159% | 62,730 |
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
- COL20A1
- Protein
- p.Pro175=
- Coding
- c.525C>T
- MANE Select
- NM_020882
- dbSNP
- rs771551505
- Type
- single nucleotide variant
- Location
- chr20:63307518 (GRCh38)
- Gene constraint
- LOEUF 1.419 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.88 · 4 PDB
Similar variants
- COL20A1 p.Thr141= Benign ★★ same type
- COL20A1 p.Ala1059Pro Uncertain significance ★ ⚠ same type
- COL20A1 p.Ala1063Thr Uncertain significance ★ ⚠ same type
- COL20A1 p.Ala1244Ser Uncertain significance ★ ⚠ same type
- COL20A1 p.Ala1265Thr Uncertain significance ★ ⚠ same type
- COL20A1 p.Ala274Thr Uncertain significance ★ ⚠ same type
- COL20A1 p.Ala300Thr Uncertain significance ★ ⚠ same type
- COL20A1 p.Ala312Thr Uncertain significance ★ ⚠ 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/col20a1-p-pro175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown