CPS1 p.Ser1090fs
c.3269_3282del · VCV4712278
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
carbamoyl phosphate synthetase I deficiency disease
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 26 of 38 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CPS1
- Protein
- p.Ser1090fs
- Coding
- c.3269_3282del
- MANE Select
- NM_001875
- Type
- Deletion
- Location
- chr2:210647987 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.80 · 14 PDB
- Residue 1090
- a modified residue (phosphoserine); an α-helix
Disease context
carbamoyl phosphate synthetase I deficiency disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Carbamoyl-phosphate synthetase 1 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- All ages
Similar variants
- CPS1 p.Ala907fs Pathogenic/Likely pathogenic ★★ same condition
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- CPS1 p.Arg932_Leu933insTer Pathogenic ★★ same condition
- CPS1 p.Asp1304fs Pathogenic ★★ same condition
- CPS1 p.Asp642fs Pathogenic/Likely pathogenic ★★ same condition
- CPS1 p.Cys644fs Pathogenic ★★ same condition
- CPS1 p.Glu455fs Pathogenic ★★ same condition
- CPS1 p.Glu842fs 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/cps1-p-ser1090fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown