BMP5 c.1104+2del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Microtia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 0.91, phastCons 1 |
| Non-coding constraint | Z -1.88 | 1 kb window · o/e 1.15 · regional · uncalibrated |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- BMP5
- Coding
- c.1104+2del
- MANE Select
- NM_021073
- Type
- Deletion
- Location
- chr6:55760455 (GRCh38)
- Gene constraint
- LOEUF 0.711 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.85
Similar variants
- BMP5 p.Gly30fs Likely 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/bmp5-c-1104-plus-2del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown