COL4A4 p.Lys514fs
c.1541_1542del · VCV3640310
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 22 of 48 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- COL4A4
- Protein
- p.Lys514fs
- Coding
- c.1541_1542del
- MANE Select
- NM_000092
- Type
- Deletion
- Location
- chr2:227088734 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 49.03 · 2 PDB
- Residue 514
- the 'triple-helical region' region; the 'disordered' region
Similar variants
- COL4A4 c.1321_1369+3del Pathogenic/Likely pathogenic ★★ same type
- COL4A4 c.2385del Pathogenic/Likely pathogenic ★★ same type
- COL4A4 c.327+1_327+5del Likely pathogenic ★★ same type
- COL4A4 c.4091-8_4092del Likely pathogenic ★★ same type
- COL4A4 c.4216+1del Likely pathogenic ★★ same type
- COL4A4 c.71+1del Pathogenic/Likely pathogenic ★★ same type
- COL4A4 c.914_930+29del Pathogenic/Likely pathogenic ★★ same type
- COL4A4 p.Ala1573fs 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/col4a4-p-lys514fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown