COL4A2 p.Pro123=
c.369G>A · rs769155086 · VCV2963165
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00596%, amr)
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 -12 | GERP -2.5 |
| Overall | ||
| CADD | 0.434 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00596%
Admixed American · 3/50,306 alleles
Filtering AF
0.00158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0011%
Overall
0.00184%
29/1,571,836 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00596% | 16,769 |
| European (non-Finnish) | 0.00198% | 50,604 |
| Remaining individualsnot grpmax-eligible | 0.00165% | 60,726 |
| African / African-American | 0.0014% | 71,570 |
| South Asian | 0.00117% | 85,502 |
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
- COL4A2
- Protein
- p.Pro123=
- Coding
- c.369G>A
- MANE Select
- NM_001846
- dbSNP
- rs769155086
- Type
- single nucleotide variant
- Location
- chr13:110428475 (GRCh38)
- Gene constraint
- LOEUF 0.618 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.97 · 4 PDB
- Residue 123
- the 'disordered' region
Similar variants
- COL4A2 p.Pro123Arg Uncertain significance ★ ⚠ same residue
- COL4A2 p.Pro123Leu Uncertain significance ★ ⚠ same residue
- COL4A2 c.361-1G>A Pathogenic/Likely pathogenic ★★ same type
- COL4A2 p.Gly1389Arg Pathogenic/Likely pathogenic ★★ same type
- COL4A2 p.Gly619Asp Likely pathogenic ★★ same type
- COL4A2 c.2425+3G>A Uncertain significance ★★ same type
- COL4A2 c.315+5G>A Uncertain significance ★★ same type
- COL4A2 c.726+4A>G 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/col4a2-p-pro123 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown