SHANK2 p.Ser802fs
c.2404_2420del · VCV3337614
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 in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 22 of 26 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -4.5 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SHANK2
- Protein
- p.Ser802fs
- Coding
- c.2404_2420del
- MANE Select
- NM_012309
- Type
- Deletion
- Location
- chr11:70492354 (GRCh38)
- Gene constraint
- LOEUF 0.417 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.58 · 2 PDB
- Residue 802
- the 'disordered' region
Similar variants
- SHANK2 p.Leu1726fs Pathogenic/Likely pathogenic ★★ same type
- SHANK2 p.Ala1384fs Likely pathogenic ★ same type
- SHANK2 p.Asp1535fs Pathogenic ★ same type
- SHANK2 p.Asp669fs Likely pathogenic ★ same type
- SHANK2 p.Glu1409fs Likely pathogenic ★ same type
- SHANK2 p.Glu581fs Likely pathogenic ★ same type
- SHANK2 p.Leu136fs Likely pathogenic ★ same type
- SHANK2 p.Leu1434_Ser1435insTer 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/shank2-p-ser802fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown