COL4A2 p.Pro940=
c.2820C>T · rs374749394 · VCV2065297
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0461%, sas)
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 -16 | GERP -3.1 |
| Overall | ||
| CADD | 0.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0461%
South Asian · 42/91,074 alleles
Filtering AF
0.035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0311%
Overall
0.00595%
96/1,614,144 alleles · ultra-rare
exomes 80/1,461,872 · genomes 16/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0461% | 2,168 |
| East Asian | 0.0312% | 3,206 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| African / African-American | 0.00933% | 10,720 |
| Admixed American | 0.00833% | 12,002 |
| European (non-Finnish) | 0.00186% | 53,637 |
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.Pro940=
- Coding
- c.2820C>T
- MANE Select
- NM_001846
- dbSNP
- rs374749394
- Type
- single nucleotide variant
- Location
- chr13:110482577 (GRCh38)
- Gene constraint
- LOEUF 0.618 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.97 · 4 PDB
- Residue 940
- the 'triple-helical region' region
Similar variants
- COL4A2 p.Pro940Leu 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
- COL4A2 p.Ala1183Val 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-pro940 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown