COL4A6 p.Ser1475=
c.4425G>A · rs149662228 · VCV1598594
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.096%, afr)
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 -10 | GERP -3.8 |
| Overall | ||
| CADD | 0.977 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.096%
African / African-American · 55/57,266 alleles
Filtering AF
0.0758%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0684%
Overall
0.00752%
91/1,209,958 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.096% | 1,041 |
| Middle Eastern | 0.046% | 2,175 |
| Remaining individualsnot grpmax-eligible | 0.0189% | 5,290 |
| Admixed American | 0.00873% | 11,452 |
| East Asian | 0.00297% | 33,725 |
| European (non-Finnish) | 0.00212% | 47,110 |
| South Asian | 0.00176% | 56,708 |
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
- COL4A6
- Protein
- p.Ser1475=
- Coding
- c.4425G>A
- MANE Select
- NM_033641
- dbSNP
- rs149662228
- Type
- single nucleotide variant
- Location
- chrX:108160563 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 1475
- the collagen iv nc1 domain
Similar variants
- COL4A6 c.3970+5G>A Uncertain significance ★★ same type
- COL4A6 p.Ala1275Thr Uncertain significance ★★ ⚠ same type
- COL4A6 p.Ala398Ser Uncertain significance ★★ ⚠ same type
- COL4A6 p.Ala421Gly Uncertain significance ★★ ⚠ same type
- COL4A6 p.Ala748Val Uncertain significance ★★ ⚠ same type
- COL4A6 p.Ala886Thr Uncertain significance ★★ ⚠ same type
- COL4A6 p.Arg1025Trp Uncertain significance ★★ ⚠ same type
- COL4A6 p.Arg1262Gln 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/col4a6-p-ser1475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown