COL4A6 p.Ser882=
c.2646T>G · rs771565093 · VCV1316327
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, nfe)
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 -0.59 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 1.031 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
European (non-Finnish) · 106/895,247 alleles
Filtering AF
0.00998%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0093%
Overall
0.00926%
112/1,209,955 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0118% | 8,446 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,846 |
| African / African-American | 0.00522% | 19,156 |
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.Ser882=
- Coding
- c.2646T>G
- MANE Select
- NM_033641
- dbSNP
- rs771565093
- Type
- single nucleotide variant
- Location
- chrX:108176881 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 882
- the 'triple-helical region' region
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-ser882 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown