COL4A6 p.Pro949=
c.2847G>A · VCV4744479
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0936%, sas)
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 -11 | GERP -3.1 |
| Overall | ||
| CADD | 0.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0936%
South Asian · 49/52,337 alleles
Filtering AF
0.0727%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0653%
Overall
0.0103%
123/1,189,238 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0936% | 1,068 |
| Remaining individualsnot grpmax-eligible | 0.0107% | 9,352 |
| European (non-Finnish) | 0.00745% | 13,423 |
| African / African-American | 0.00356% | 28,063 |
| Finnishnot grpmax-eligible | 0.00216% | 46,260 |
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.Pro949=
- Coding
- c.2847G>A
- MANE Select
- NM_033641
- Type
- single nucleotide variant
- Location
- chrX:108175199 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 949
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A6 p.Pro949Leu 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
- COL4A6 p.Arg1025Trp 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-pro949 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown