COL4A3 p.Pro987=
c.2961C>T · rs375523118 · VCV1129879
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, 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 -0.067 | GERP -4.4, phastCons 0.02 |
| Overall | ||
| CADD | 7.481 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,080 alleles
Filtering AF
0.00922%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.00663%
107/1,613,400 alleles · ultra-rare
exomes 94/1,461,304 · genomes 13/152,096 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,080 |
| African / African-American | 0.016% | 6,239 |
| European (non-Finnish) | 0.0078% | 12,823 |
| Admixed American | 0.00334% | 29,969 |
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.Pro987=
- Coding
- c.2961C>T
- MANE Select
- NM_000091
- dbSNP
- rs375523118
- Type
- single nucleotide variant
- Location
- chr2:227289229 (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 987
- 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-pro987 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown