COL4A3 p.Pro9=
c.27G>A · rs918717650 · VCV1137834
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0084%, 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 0.2 | GERP 0.17 |
| Overall | ||
| CADD | 5.845 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0084%
African / African-American · 6/71,420 alleles
Filtering AF
0.00361%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00248%
Overall
0.000524%
8/1,525,998 alleles · very rare
exomes 6/1,373,950 · genomes 2/152,048 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0084% | 11,903 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00353% | 28,350 |
| South Asian | 0.0012% | 83,310 |
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
- COL4A3
- Protein
- p.Pro9=
- Coding
- c.27G>A
- MANE Select
- NM_000091
- dbSNP
- rs918717650
- Type
- single nucleotide variant
- Location
- chr2:227164753 (GRCh38)
- Gene constraint
- LOEUF 0.709 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 48.64 · 2 PDB
Similar variants
- COL4A3 p.Pro9Leu Uncertain significance ★★ ⚠ same residue
- COL4A3 p.Pro9Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL4A3 c.1114+1G>A Likely pathogenic ★★ same type
- COL4A3 c.1114+2T>C Pathogenic/Likely pathogenic ★★ same type
- COL4A3 c.1408+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL4A3 c.1408+1G>C Pathogenic/Likely pathogenic ★★ same type
- COL4A3 c.1504+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL4A3 c.1927+1G>A 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/col4a3-p-pro9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown