# NM_001807.6(CEL):c.959C>T (p.Pro320Leu)

https://sugi.bio/variant/cel-p-pro320leu

## Summary

**CEL p.Pro320Leu (c.959C>T)** is classified **Uncertain significance** in CEL (ClinVar, Single submitter, 1 submitter). Ultra-rare (popmax 0.0247%, eas); Associated with maturity-onset diabetes of the young type 8.

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · 1 linked condition · ultra-rare (popmax 0.0247%, eas)

## For patients & families {#patients}

This is a change in the CEL gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to maturity-onset diabetes of the young type 8.

*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 dominant, Not applicable |
| Age of onset (of this condition) | Adolescent, Adult, Childhood |
| Prevalence | 1-5 / 10 000 (Europe) |
| Diagnostic panels | CEL is a diagnostic-grade gene on 2 Genomics England panels |

**Commonly reported features of MODY** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Glucose intolerance — Frequent (79-30%)
- Hyperglycemia — Frequent (79-30%)
- Glycosuria — Frequent (79-30%)
- Abnormal oral glucose tolerance — Frequent (79-30%)
- Abnormal C-peptide level — Frequent (79-30%)
- Abnormal circulating insulin concentration — Frequent (79-30%)
- Hypoinsulinemia — Frequent (79-30%)
- Elevated hemoglobin A1c — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010662/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CEL](https://sugi.bio/atlas/gene/CEL/) |
| Protein change (HGVS p.) | p.Pro320Leu |
| Coding change (HGVS c.) | c.959C>T |
| MANE Select transcript | [NM_001807](https://www.ncbi.nlm.nih.gov/nuccore/NM_001807) |
| Variant type | single nucleotide variant |
| Location | chr9:133068735-133068735 (GRCh38) |
| ClinVar | [VCV3382935](https://www.ncbi.nlm.nih.gov/clinvar/variation/3382935/) |

**All HGVS expressions:** `NC_000009.11:g.135944122C>T`, `NC_000009.12:g.133068735C>T`, `NG_016394.1:g.11758C>T`, `NM_001807.6:c.959C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 7.681, GERP 1.57, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 26.9**. 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 0.22** across the covering region of the MANE Select transcript (133,068,675–133,068,833), spanning 158 bp — the region is depleted of missense variation. Chi-square p 2.1e-12. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>A, Δ0.55 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.0247%** (eas) · FAF95 0.0138% · FAF99 0.0106% · 11/44,516 in the highest group · 26/1,606,954 alleles overall — ultra-rare (popmax 0.0247%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0247% | 4,047 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.00678% | 14,758 |
| African / African-American | 0.00544% | 18,367 |
| South Asian | 0.00111% | 89,712 |
| European (non-Finnish) | 0.000679% | 147,170 |

*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}

**CEL** population constraint: LOEUF 0.972, pLI 3.4493e-10, missense-Z 1.4207. *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):

- **maturity-onset diabetes of the young type 8** — Moderate (AD)

## Protein context {#protein}

Residue **320** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 84.10, 69% of residues very-high.

**7 experimental structure(s)** (PDB): [1F6W](https://www.rcsb.org/structure/1F6W), [1JMY](https://www.rcsb.org/structure/1JMY), [6H0T](https://www.rcsb.org/structure/6H0T), [6H0V](https://www.rcsb.org/structure/6H0V), [6H18](https://www.rcsb.org/structure/6H18), [6H19](https://www.rcsb.org/structure/6H19).

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

*Describes the biological roles of CEL (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.*


### Pathways affected {#pathways}

CEL participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Developmental Lineage of Pancreatic Acinar Cells](https://reactome.org/content/detail/R-HSA-9925561) | curated |
| [Digestion of dietary lipid](https://reactome.org/content/detail/R-HSA-192456) | curated |

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

**Biological process:** pancreatic juice secretion, intestinal cholesterol absorption.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Juno Genomics, Hangzhou Juno Genomics, Inc | Uncertain significance | criteria provided, single submitter | clinical testing |  |

## Associated conditions {#conditions}

[maturity-onset diabetes of the young type 8](https://sugi.bio/atlas/disease/maturity-onset-diabetes-of-the-young-type-8/).

**Reported phenotype names (ClinVar):** Maturity-onset diabetes of the young type 8, DIABETES AND PANCREATIC EXOCRINE DYSFUNCTION, DIABETES-PANCREATIC EXOCRINE DYSFUNCTION SYNDROME.

## Similar variants {#similar}

Related CEL variant pages (same residue, condition, or type): [CEL c.67-3C>A](/variant/cel-c-67-minus-3c-a), [CEL p.Ala295Ser](/variant/cel-p-ala295ser), [CEL p.Ala548Glu](/variant/cel-p-ala548glu), [CEL p.Ala722Val](/variant/cel-p-ala722val), [CEL p.Arg116Gln](/variant/cel-p-arg116gln), [CEL p.Arg185Trp](/variant/cel-p-arg185trp), [CEL p.Arg443Trp](/variant/cel-p-arg443trp), [CEL p.Asn37Ser](/variant/cel-p-asn37ser).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 3382935). 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.*