CSN3
protein-codingcasein kappa
Gene summary
Involved in lactation and protein stabilization. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]
- CSN10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CSN3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001394997.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 28 | 2 | 30 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 2 | 0 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001381926.1 | 3 | MANE Select | |
| Ensembl | ENSP00000304822.3 | 3 | MANE Select | |
| RefSeq | NP_005203.2 | 3 | Standard | |
| Ensembl | ENSP00000508633.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Splicing factor NOVA regulated synaptic proteins
Biological Process
- lactation
- protein stabilization
- transmembrane transport
Molecular Function
- molecular_function
- protein binding
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000304954
- Coding exons
- 3
- Length
- 8841
- Individuals with no LoFs
- 125586
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125589
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0267 | 105 | 104 | 1.01 | 0.00000564 | 1155 |
| Missense (PolyPhen) | 3 | 4.278 | 0.70127 | 41 | ||
| Synonymous | -0.859 | 44 | 37.3 | 1.18 | 0.00000185 | 384 |
| Loss of Function | 0.475 | 3 | 4.03 | 0.744 | 1.68e-7 | 57 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000096 | 0.0000088 | rare |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Kappa-casein stabilizes micelle formation, preventing casein precipitation in milk.;
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- LoFtool
- 0.792
- RVIS EVS
- 1.13
- RVIS percentile EVS
- 92.16
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0329
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |