COL4A6 p.Phe1453=
c.4359C>T · rs139555294 · VCV499492
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.157%, 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 -6.9 | GERP -3.5 |
| Overall | ||
| CADD | 0.199 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.157%
African / African-American · 90/57,339 alleles
Filtering AF
0.131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.121%
Overall
0.00845%
102/1,207,786 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.157% | 637 |
| Remaining individualsnot grpmax-eligible | 0.00842% | 11,880 |
| Admixed American | 0.00659% | 15,172 |
| East Asian | 0.00593% | 16,867 |
| South Asian | 0.00178% | 56,070 |
| European (non-Finnish) | 0.000224% | 447,067 |
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.Phe1453=
- Coding
- c.4359C>T
- MANE Select
- NM_033641
- dbSNP
- rs139555294
- Type
- single nucleotide variant
- Location
- chrX:108160629 (GRCh38)
- Structure
- AlphaFold pLDDT 48.27
- Residue 1453
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A6 p.Phe1453Ser 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-phe1453 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown