COL4A5 p.Phe625=
c.1875C>T · rs1239337307 · VCV2188282
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0241%, mid)
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 0.5 | GERP -0.95, phastCons 1 |
| Overall | ||
| CADD | 12.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0241%
Middle Eastern · 1/4,153 alleles
Filtering AF
0.000579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000217%
Overall
0.000331%
4/1,209,648 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0241% | 4,153 |
| African / African-American | 0.00349% | 28,661 |
| European (non-Finnish) | 0.000112% | 894,775 |
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
- COL4A5
- Protein
- p.Phe625=
- Coding
- c.1875C>T
- MANE Select
- NM_033380
- dbSNP
- rs1239337307
- Type
- single nucleotide variant
- Location
- chrX:108598797 (GRCh38)
- Structure
- AlphaFold pLDDT 49.04 · 2 PDB
- Residue 625
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A5 p.Phe625Val Uncertain significance ★★ ⚠ same residue
- COL4A5 c.1032+1G>C Pathogenic/Likely pathogenic ★★ same type
- COL4A5 c.1033-1G>A Pathogenic ★★ same type
- COL4A5 c.1033-2A>G Pathogenic/Likely pathogenic ★★ same type
- COL4A5 c.1339+1G>A Pathogenic/Likely pathogenic ★★ same type
- COL4A5 c.141+1G>A Pathogenic ★★ same type
- COL4A5 c.1423+1G>A Pathogenic ★★ same type
- COL4A5 c.1424-20T>A Pathogenic/Likely pathogenic ★★ 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/col4a5-p-phe625 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown