CPS1 p.Asp641=
c.1923T>C · rs149489502 · VCV1673929
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 2.9, phastCons 1 |
| Overall | ||
| CADD | 11.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CPS1
- Protein
- p.Asp641=
- Coding
- c.1923T>C
- MANE Select
- NM_001875
- dbSNP
- rs149489502
- Type
- single nucleotide variant
- Location
- chr2:210605188 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.80 · 14 PDB
- Residue 641
- the atp-grasp 1 domain
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 c.1086+1G>A Likely pathogenic ★★ same condition
- CPS1 c.1087-1G>T Pathogenic/Likely pathogenic ★★ same condition
- CPS1 c.1165-2A>G Likely pathogenic ★★ same condition
- CPS1 c.1263+5G>C Pathogenic/Likely pathogenic ★★ same condition
- CPS1 c.1549+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CPS1 c.1549+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CPS1 c.1837-8A>G Pathogenic/Likely pathogenic ★★ same condition
- CPS1 c.1981+1G>C 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-asp641 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown