SETD5 p.Ser1364fs
c.4088dup · VCV4864354
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Inborn genetic diseases
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 (23 of 23) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- SETD5
- Protein
- p.Ser1364fs
- Coding
- c.4088dup
- MANE Select
- NM_001080517
- Type
- Duplication
- Location
- chr3:9475849 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.10
- Residue 1364
- a UniProt-annotated variant site (in mrd23); the 'disordered' region
Similar variants
- SETD5 p.Asp826fs Pathogenic ★ same condition
- SETD5 p.Ser819_Ile820insSer Likely benign ★ same condition
- SETD5 c.2347-7A>G Pathogenic ★★ same condition
- SETD5 p.Arg1001Ter Pathogenic ★★ same condition
- SETD5 p.Arg308Ter Pathogenic/Likely pathogenic ★★ same condition
- SETD5 p.Arg361Ter Pathogenic ★★ same condition
- SETD5 p.Gln1101Ter Pathogenic ★★ same condition
- SETD5 p.Ser668Ter Pathogenic/Likely pathogenic ★★ 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/setd5-p-ser1364fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown