COL4A4 p.Cys55fs
c.163dup · VCV4884677
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
hematuria, benign familial, 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 48 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 2.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- COL4A4
- Protein
- p.Cys55fs
- Coding
- c.163dup
- MANE Select
- NM_000092
- Type
- Duplication
- Location
- chr2:227140189 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.03 · 2 PDB
- Residue 55
- the '7s domain' region
Similar variants
- COL4A4 p.Gln1105fs Pathogenic/Likely pathogenic ★★ same condition
- COL4A4 p.Gly503fs Pathogenic/Likely pathogenic ★★ same condition
- COL4A4 p.Lys437fs Pathogenic/Likely pathogenic ★★ same condition
- COL4A4 p.Lys706Ter Pathogenic/Likely pathogenic ★★ same condition
- COL4A4 p.Pro1385fs Pathogenic/Likely pathogenic ★★ same condition
- COL4A4 p.Pro99fs Pathogenic/Likely pathogenic ★★ same condition
- COL4A4 p.Cys55Phe Uncertain significance ★★ ⚠ same residue
- COL4A4 c.(1029+1_1030-1 Pathogenic ★ same condition
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/col4a4-p-cys55fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown