# NM_001875.5(CPS1):c.3304G>C (p.Ala1102Pro)

https://sugi.bio/variant/cps1-p-ala1102pro

## Summary

**CPS1 p.Ala1102Pro (c.3304G>C)** is classified **Uncertain significance** in CPS1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2025-03-31). AlphaMissense: likely benign (0.0849); Very rare (popmax 0.00133%, afr); Associated with carbamoyl phosphate synthetase I deficiency disease.

**At a glance:** Uncertain significance · review: No assertion criteria · 1 submitter · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.00133%, afr)

## For patients & families {#patients}

This is a change in the CPS1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to carbamoyl phosphate synthetase I deficiency disease.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | All ages |
| Clinical trials | 3 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | CPS1 is a diagnostic-grade gene on 9 Genomics England panels |

**Commonly reported features of Carbamoyl-phosphate synthetase 1 deficiency** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Seizure — Very frequent (99-80%)
- Hypotonia — Very frequent (99-80%)
- Episodic ammonia intoxication — Very frequent (99-80%)
- Hyperammonemia — Very frequent (99-80%)
- Respiratory insufficiency — Very frequent (99-80%)
- Aminoaciduria — Very frequent (99-80%)
- Hypoargininemia — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0007269/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CPS1](https://sugi.bio/atlas/gene/CPS1/) |
| Protein change (HGVS p.) | p.Ala1102Pro |
| Coding change (HGVS c.) | c.3304G>C |
| MANE Select transcript | [NM_001875](https://www.ncbi.nlm.nih.gov/nuccore/NM_001875) |
| Variant type | single nucleotide variant |
| Location | chr2:210648025-210648025 (GRCh38) |
| ClinVar | [VCV4065326](https://www.ncbi.nlm.nih.gov/clinvar/variation/4065326/) |

**All HGVS expressions:** `LRG_336:g.175341G>C`, `LRG_336t1:c.3304G>C`, `NC_000002.11:g.211512749G>C`, `NC_000002.12:g.210648025G>C`, `NG_008285.1:g.175341G>C`, `NM_001122633.3:c.3304G>C`, `NM_001369256.1:c.3337G>C`, `NM_001369257.1:c.3304G>C`, `NM_001875.5:c.3304G>C`, `NR_161225.1:n.4213G>C`, `NR_163592.1:n.2460G>C`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.0849)
- REVEL 0.46 (indeterminate)
- SaProt LLR -3.25 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this tolerated; REVEL makes no call
- Conservation: phyloP 3.438, GERP 0.891, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 19.31**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 0.93** across the covering region of the MANE Select transcript (210,556,734–210,677,982), spanning 121,248 bp. Chi-square p 0.0019. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00133%** (afr) · 1/75,040 in the highest group · 2/1,461,692 alleles overall — very rare (popmax 0.00133%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.00133% | 75,040 |
| European (non-Finnish) | 8.48e-05% | 1,179,912 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**CPS1** population constraint: LOEUF 0.764, pLI 1.7622e-19, missense-Z 1.7456. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **carbamoyl phosphate synthetase I deficiency disease** — Definitive (AR)

## Protein context {#protein}

Residue **1102** lies in the atp-grasp 2 domain.

AlphaFold model confidence (whole protein): pLDDT 93.80, 88% of residues very-high.

**14 experimental structure(s)** (PDB): [2YVQ](https://www.rcsb.org/structure/2YVQ), [4UTR](https://www.rcsb.org/structure/4UTR), [4UTV](https://www.rcsb.org/structure/4UTV), [4UTX](https://www.rcsb.org/structure/4UTX), [4UTZ](https://www.rcsb.org/structure/4UTZ), [4UU7](https://www.rcsb.org/structure/4UU7).

## What this gene does {#gene-function}

*Describes the biological roles of CPS1 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** CPS1's established molecular role includes carbamoyl-phosphate synthase (ammonia) activity. p.Ala1102Pro falls in the atp-grasp 2 domain. In Reactome, CPS1 is annotated in disease pathway(s) including **CPS1 variants cause CPS1 deficiency**.

**Disease mechanism (Reactome):** CPS1 loss or alteration is curated in [CPS1 variants cause CPS1 deficiency](https://reactome.org/content/detail/R-HSA-9955542).

### Pathways affected {#pathways}

CPS1 participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [CPS1 variants cause CPS1 deficiency](https://reactome.org/content/detail/R-HSA-9955542) | other |
| [Negative transcriptional regulation of urea cycle enzymes](https://reactome.org/content/detail/R-HSA-9988426) | curated |
| [Urea cycle](https://reactome.org/content/detail/R-HSA-70635) | other |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** carbamoyl-phosphate synthase (ammonia) activity, potassium ion binding, small molecule binding, metal ion binding, modified amino acid binding.

**Biological process:** triglyceride catabolic process, response to lipopolysaccharide, vasodilation, nitric oxide metabolic process, homocysteine metabolic process, carbamoyl phosphate biosynthetic process.

## Clinical significance {#significance}

**Uncertain significance** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 2025-03-31.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Natera, Inc. | Uncertain significance | no assertion criteria provided | clinical testing | 2025-03-31 |

## Associated conditions {#conditions}

[carbamoyl phosphate synthetase I deficiency disease](https://sugi.bio/atlas/disease/carbamoyl-phosphate-synthetase-i-deficiency-disease/).

**Reported phenotype names (ClinVar):** Congenital hyperammonemia, type I, CPS I DEFICIENCY, Carbamoyl phosphate synthetase 1 deficiency, Hyperammonemia due to carbamoyl phosphate synthetase 1 deficiency, CPS 1 deficiency, Carbamyl phosphate synthetase (CPS) deficiency, Carbamoyl phosphate synthetase I deficiency disease, Carbamoyl-phosphate synthase I deficiency.

## Same-residue context {#hotspot}

Residue **1102** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [CPS1 p.Ala1102fs](/variant/cps1-p-ala1102fs). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related CPS1 variant pages (same residue, condition, or type): [CPS1 p.Ala1102fs](/variant/cps1-p-ala1102fs), [CPS1 c.1086+1G>A](/variant/cps1-c-1086-plus-1g-a), [CPS1 c.1087-1G>T](/variant/cps1-c-1087-minus-1g-t), [CPS1 c.1165-2A>G](/variant/cps1-c-1165-minus-2a-g), [CPS1 c.1263+5G>C](/variant/cps1-c-1263-plus-5g-c), [CPS1 c.1549+1G>A](/variant/cps1-c-1549-plus-1g-a), [CPS1 c.1549+1G>T](/variant/cps1-c-1549-plus-1g-t), [CPS1 c.1837-8A>G](/variant/cps1-c-1837-minus-8a-g).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-07-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 4065326). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*