COL4A3 p.Pro942=
c.2826C>T · rs201064766 · VCV447170
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
rare (popmax 0.957%, mid)
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 -13 | GERP -5.1 |
| Overall | ||
| CADD | 0.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.957%
Middle Eastern · 58/6,062 alleles
Filtering AF
0.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.689%
Overall
0.0436%
703/1,614,044 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.957% | 105 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0811% | 1,233 |
| Admixed American | 0.0767% | 1,304 |
| African / African-American | 0.0746% | 1,340 |
| European (non-Finnish) | 0.0371% | 2,694 |
| South Asian | 0.0132% | 7,587 |
| East Asian | 0.00446% | 22,437 |
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.Pro942=
- Coding
- c.2826C>T
- MANE Select
- NM_000091
- dbSNP
- rs201064766
- Type
- single nucleotide variant
- Location
- chr2:227284290 (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 942
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- 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
- COL4A3 c.2224-2A>G 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-pro942 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown