COL4A1 p.Pro68=
c.204T>A · rs370425696 · VCV1157197
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0108%, 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 -9.3 | GERP -3.2 |
| Overall | ||
| CADD | 0.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0108%
European (non-Finnish) · 127/1,180,004 alleles
Filtering AF
0.00919%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00863%
Overall
0.00889%
130/1,461,890 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0108% | 9,291 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
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
- COL4A1
- Protein
- p.Pro68=
- Coding
- c.204T>A
- MANE Select
- NM_001845
- dbSNP
- rs370425696
- Type
- single nucleotide variant
- Location
- chr13:110213956 (GRCh38)
- Gene constraint
- LOEUF 0.238 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 49.43 · 4 PDB
- Residue 68
- the 'disordered' region
Similar variants
- COL4A1 c.1085-2A>G Likely pathogenic ★★ same type
- COL4A1 c.1991-2A>G Likely pathogenic ★★ same type
- COL4A1 c.2458+1G>A Pathogenic ★★ same type
- COL4A1 c.2458+2T>C Pathogenic/Likely pathogenic ★★ same type
- COL4A1 c.3742+1G>A Pathogenic ★★ same type
- COL4A1 c.388-1G>C Pathogenic/Likely pathogenic ★★ same type
- COL4A1 c.4150+1G>A Pathogenic ★★ same type
- COL4A1 c.4250-1G>A 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/col4a1-p-pro68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown