COL4A5 p.Pro668=
c.2004T>G · rs376003159 · VCV1528647
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0124%, afr)
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 · T>A here scores Δ0.39 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.77 | GERP 0.21, phastCons 1 |
| Overall | ||
| CADD | 10.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0124%
African / African-American · 7/56,514 alleles
Filtering AF
0.00573%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00409%
Overall
0.000581%
7/1,204,699 alleles · ultra-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
- COL4A5
- Protein
- p.Pro668=
- Coding
- c.2004T>G
- MANE Select
- NM_033380
- dbSNP
- rs376003159
- Type
- single nucleotide variant
- Location
- chrX:108601448 (GRCh38)
- Structure
- AlphaFold pLDDT 49.04 · 2 PDB
- Residue 668
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A5 p.Pro668Leu Uncertain significance ★★ ⚠ same residue
- COL4A5 p.Pro668Ser Uncertain significance ★ ⚠ same residue
- COL4A5 c.1032+1G>C Pathogenic/Likely pathogenic ★★ same type
- COL4A5 c.1033-1G>A Pathogenic ★★ same type
- COL4A5 c.1033-2A>G Pathogenic/Likely pathogenic ★★ same type
- COL4A5 c.1339+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL4A5 c.141+1G>A Pathogenic ★★ same type
- COL4A5 c.1423+1G>A 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/col4a5-p-pro668 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown