COL4A1 p.Pro1007=
c.3021G>A · rs148308759 · VCV1670643
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00333%, 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 -0.17 | GERP -3.5, phastCons 0.008 |
| Overall | ||
| CADD | 6.989 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,004 alleles
Filtering AF
0.00138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00116%
Overall
0.0018%
29/1,613,920 alleles · very rare
exomes 28/1,461,734 · genomes 1/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,002 |
| South Asian | 0.00329% | 30,358 |
| European (non-Finnish) | 0.00203% | 49,163 |
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
- COL4A1
- Protein
- p.Pro1007=
- Coding
- c.3021G>A
- MANE Select
- NM_001845
- dbSNP
- rs148308759
- Type
- single nucleotide variant
- Location
- chr13:110176461 (GRCh38)
- Gene constraint
- LOEUF 0.238 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 49.43 · 4 PDB
- Residue 1007
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A1 p.Pro1007Leu Uncertain significance ★★ ⚠ same residue
- COL4A1 p.Pro1007Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- COL4A1 c.1085-2A>G Likely pathogenic ★★ same type
- COL4A1 c.1991-2A>G Likely pathogenic ★★ same type
- COL4A1 c.2458+1G>A Pathogenic ★★ same type
- COL4A1 c.2458+2T>C Pathogenic/Likely pathogenic ★★ same type
- COL4A1 c.3742+1G>A Pathogenic ★★ same type
- COL4A1 c.388-1G>C Pathogenic/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/col4a1-p-pro1007 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown