SYN1 p.Ser96fs
c.288del · rs1603078614 · VCV817226
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 13 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 1.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SYN1
- Protein
- p.Ser96fs
- Coding
- c.288del
- MANE Select
- NM_006950
- dbSNP
- rs1603078614
- Type
- Deletion
- Location
- chrX:47619441 (GRCh38)
- Structure
- AlphaFold pLDDT 69.86
- Residue 96
- the 'b; linker' region
Similar variants
- SYN1 p.Asn334fs Pathogenic ★★ same type
- SYN1 p.Met1fs Pathogenic/Likely pathogenic ★★ same type
- SYN1 p.His38_Ala42del Uncertain significance ★★ same type
- SYN1 c.1056-14_1056-8del Benign ★★ same type
- SYN1 c.980+43_981del Pathogenic ★ same type
- SYN1 p.Ala577fs Pathogenic ★ same type
- SYN1 p.Ala676fs Likely pathogenic ★ same type
- SYN1 p.Ala83fs 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/syn1-p-ser96fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown