CPS1 c.2829+3A>G
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.13%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.61 | donor loss · deltas |
| Pangolin | Δ0.45 | loss · gain 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 0.49, phastCons 1 |
| Non-coding constraint | Z 0.93 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 13.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.13%
South Asian · 118/91,072 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.00768%
124/1,613,836 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.13% | 772 |
| Middle Eastern | 0.0333% | 3,006 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| African / African-American | 0.00133% | 75,040 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CPS1
- Coding
- c.2829+3A>G
- MANE Select
- NM_001875
- Type
- single nucleotide variant
- Location
- chr2:210637846 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.80 · 14 PDB
Similar variants
- CPS1 c.1086+1G>A Likely pathogenic ★★ same type
- CPS1 c.1087-1G>T Pathogenic/Likely pathogenic ★★ same type
- CPS1 c.1165-2A>G Likely pathogenic ★★ same type
- CPS1 c.1263+5G>C Pathogenic/Likely pathogenic ★★ same type
- CPS1 c.1549+1G>A Pathogenic/Likely pathogenic ★★ same type
- CPS1 c.1549+1G>T Pathogenic/Likely pathogenic ★★ same type
- CPS1 c.1837-8A>G Pathogenic/Likely pathogenic ★★ same type
- CPS1 c.1981+1G>C 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/cps1-c-2829-plus-3a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown