COL4A3 p.Pro429=
c.1287A>G · rs2469634969 · VCV2847821
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -3 |
| Overall | ||
| CADD | 1.319 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- COL4A3
- Protein
- p.Pro429=
- Coding
- c.1287A>G
- MANE Select
- NM_000091
- dbSNP
- rs2469634969
- Type
- single nucleotide variant
- Location
- chr2:227263916 (GRCh38)
- Gene constraint
- LOEUF 0.709 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 48.64 · 2 PDB
- Residue 429
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A3 p.Pro429fs Pathogenic ★ 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
- COL4A3 c.2020+1G>T 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-pro429 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown