COL15A1 p.Val668=
c.2004T>C · rs758748658 · VCV747970
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, 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 -0.15 | GERP -3, phastCons 0.004 |
| Overall | ||
| CADD | 7.901 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,904 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.000434%
7/1,612,928 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00668% | 14,981 |
| European (non-Finnish) | 0.00017% | 589,828 |
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
- COL15A1
- Protein
- p.Val668=
- Coding
- c.2004T>C
- MANE Select
- NM_001855
- dbSNP
- rs758748658
- Type
- single nucleotide variant
- Location
- chr9:99025927 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.68 · 1 PDB
- Residue 668
- the collagen-like 1 domain; the 'disordered' region; the 'triple-helical region 2 (col2)' region
Similar variants
- COL15A1 p.Leu756= Benign ★★ same type
- COL15A1 p.Pro1063Leu Benign ★★ ⚠ same type
- COL15A1 p.Ser218= Benign ★★ same type
- COL15A1 p.Ala1006Ser Uncertain significance ★ ⚠ same type
- COL15A1 p.Ala1115Val Uncertain significance ★ ⚠ same type
- COL15A1 p.Ala1148Thr Uncertain significance ★ ⚠ same type
- COL15A1 p.Ala1193Val Uncertain significance ★ ⚠ same type
- COL15A1 p.Ala1244Ser 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/col15a1-p-val668 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown