F11 c.55+1del
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 +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.62 | GERP -2.9, phastCons 1 |
| Non-coding constraint | Z 3.02 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 35.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- F11
- Coding
- c.55+1del
- MANE Select
- NM_001322131 · reported on NM_000128
- dbSNP
- rs1191677538
- Type
- Deletion
- Location
- chr4:186267191 (GRCh38)
- Structure
- AlphaFold pLDDT 68.98
Similar variants
- F11 c.1136-7_1136-4del Pathogenic ★★ same type
- F11 p.Gly303fs Pathogenic ★★ same type
- F11 p.Ile215_Asp216del Pathogenic/Likely pathogenic ★★ same type
- F11 p.Ile359fs Pathogenic ★★ same type
- F11 p.Ile481fs Pathogenic ★★ same type
- F11 p.Leu442fs Pathogenic ★★ same type
- F11 p.Leu483fs Pathogenic/Likely pathogenic ★★ same type
- F11 p.Tyr115fs 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/f11-c-55-plus-1del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown