COL4A2 p.Pro1551=
c.4653T>C · rs748405164 · VCV2994609
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0198%, sas)
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 Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.8 |
| Overall | ||
| CADD | 1.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0198%
South Asian · 18/91,088 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0105%
Overall
0.00217%
35/1,614,066 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0198% | 5,060 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| European (non-Finnish) | 0.00119% | 84,289 |
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.Pro1551=
- Coding
- c.4653T>C
- MANE Select
- NM_001846
- dbSNP
- rs748405164
- Type
- single nucleotide variant
- Location
- chr13:110507993 (GRCh38)
- Gene constraint
- LOEUF 0.618 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.97 · 4 PDB
- Residue 1551
- the collagen iv nc1 domain; a turn
Similar variants
- 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
- COL4A2 p.Ala1183Val Uncertain significance ★★ ⚠ same type
- COL4A2 p.Ala1363Val 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-pro1551 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown