CSN1S1
protein-codingcasein alpha s1
Gene summary
Predicted to be involved in several processes, including response to 11-deoxycorticosterone; response to dehydroepiandrosterone; and response to progesterone. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]
- CASA
- CSN1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.5 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 CSN1S1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001890.2. 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 | 16 | 1 | 17 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 16 | 1 | 0 | 17 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001881.1 | 15 | MANE Select | |
| Ensembl | ENSP00000246891.4 | 15 | MANE Select | |
| RefSeq | NP_001020275.1 | 14 | Standard | |
| Ensembl | ENSP00000426684.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- response to estradiol
- response to progesterone
- transmembrane transport
- response to dehydroepiandrosterone
- response to 11-deoxycorticosterone
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000246891
- Coding exons
- 14
- Length
- 15491
- Individuals with no LoFs
- 124472
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 50
- Defined
- 124522
- p
- 0.000201
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.319 | 80 | 88.5 | 0.904 | 0.00000432 | 1207 |
| Missense (PolyPhen) | 12 | 14.338 | 0.83692 | 165 | ||
| Synonymous | 0.145 | 28 | 29.0 | 0.966 | 0.00000160 | 291 |
| Loss of Function | -0.850 | 22 | 18.1 | 1.22 | 7.69e-7 | 238 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00023 | 0.00022 | rare |
| Finnish | 0.00015 | 0.00014 | rare |
| European (Non-Finnish) | 0.00039 | 0.00034 | rare |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0.00018 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Important role in the capacity of milk to transport calcium phosphate.;
Intolerance Scores
- LoFtool
- 0.868
- RVIS EVS
- 1.02
- RVIS percentile EVS
- 90.86
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0427
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |