SRCAP p.Ser2416fs
c.7245_7246del · VCV3340716
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 | escapes | premature termination codon in the last exon (34 of 34) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -1.9, phastCons 0.001 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SRCAP
- Protein
- p.Ser2416fs
- Coding
- c.7245_7246del
- MANE Select
- NM_006662
- Type
- Microsatellite
- Location
- chr16:30737283 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 2416
- the 'disordered' region; a UniProt-annotated variant site (in dehmba); a UniProt-annotated variant site (in flhs)
Similar variants
- SRCAP p.Ser2416= Conflicting classifications of pathogenicity ★ same residue
- SRCAP p.Ser2416Cys Uncertain significance ★ ⚠ same residue
- SRCAP p.Gln2770del Uncertain significance ★★ same type
- SRCAP p.Glu3182del Uncertain significance ★★ same type
- SRCAP p.Pro2488del Uncertain significance ★★ same type
- SRCAP p.Ser2576del Uncertain significance ★★ same type
- SRCAP p.2992TVT[1] Benign/Likely benign ★★ same type
- SRCAP p.Glu180fs 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/srcap-p-ser2416fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown