COL4A6 p.Val952=
c.2856C>T · rs183856005 · VCV682346
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0274%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -3.1 |
| Overall | ||
| CADD | 0.043 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0274%
East Asian · 9/32,805 alleles
Filtering AF
0.0142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0107%
Overall
0.0041%
49/1,194,124 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0274% | 3,645 |
| Finnishnot grpmax-eligible | 0.0129% | 7,726 |
| African / African-American | 0.00532% | 18,788 |
| Remaining individualsnot grpmax-eligible | 0.00426% | 23,498 |
| European (non-Finnish) | 0.00315% | 31,717 |
| South Asian | 0.00187% | 53,354 |
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.Val952=
- Coding
- c.2856C>T
- MANE Select
- NM_033641
- dbSNP
- rs183856005
- Type
- single nucleotide variant
- Location
- chrX:108175190 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 952
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A6 p.Val952Phe 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-val952 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown