COL4A6 p.Arg1025=
c.3075G>A · rs760323641 · VCV1984561
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00067%, 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 -1.1 | GERP -2 |
| Overall | ||
| CADD | 1.636 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00067%
European (non-Finnish) · 6/895,228 alleles
Filtering AF
0.000241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000158%
Overall
0.000547%
6/1,097,654 alleles · very rare
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.Arg1025=
- Coding
- c.3075G>A
- MANE Select
- NM_033641
- dbSNP
- rs760323641
- Type
- single nucleotide variant
- Location
- chrX:108174503 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 1025
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A6 p.Arg1025Trp Uncertain significance ★★ ⚠ same residue
- COL4A6 p.Arg1025Gln Uncertain significance ★ ⚠ same residue
- 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
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-arg1025 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown