IGSF1 p.Pro779fs
c.2333dup · VCV4849597
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Paediatric disorders
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 14 of 20 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.1 | GERP -4.1, phastCons 0.97 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- IGSF1
- Protein
- p.Pro779fs
- Coding
- c.2333dup
- MANE Select
- NM_001555
- Type
- Duplication
- Location
- chrX:131277213 (GRCh38)
- Structure
- AlphaFold pLDDT 73.64
- Residue 779
- the ig-like c2-type 8 domain
Disease context
Paediatric disorders
Similar variants
- IGSF1 p.Val89fs Pathogenic ★ same condition
- IGSF1 c.1646+2del Likely pathogenic ★ same condition
- IGSF1 p.Arg794Ter Pathogenic ★ same condition
- IGSF1 p.Arg992Ter Pathogenic ★ same condition
- IGSF1 p.Tyr945Ter Likely pathogenic ★ same condition
- IGSF1 p.Trp1237Ser Uncertain significance ⚠ same condition
- IGSF1 c.2320+6G>A Likely benign same condition
- IGSF1 p.Ala1008= Likely benign 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/igsf1-p-pro779fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown