CSAD
protein-codingcysteine sulfinic acid decarboxylase
Gene summary
This gene encodes a member of the group 2 decarboxylase family. A similar protein in rodents plays a role in multiple biological processes as the rate-limiting enzyme in taurine biosynthesis, catalyzing the decarboxylation of cysteinesulfinate to hypotaurine. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.3 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 CSAD variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001244705.2. 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 | 2 | 2 | 3 | 7 | ||
| missense | 70 | 1 | 71 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 75 | 3 | 3 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001231634.1 | 14 | MANE Select | |
| Ensembl | ENSP00000415485.1 | 14 | MANE Select | |
| RefSeq | NP_001231635.1 | 8 | Standard | |
| RefSeq | NP_057073.4 | 16 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| csad | Danio rerio | Structure: whole organism Quality: dead abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Taurine and hypotaurine metabolism - Homo sapiens (human)
- Taurine and Hypotaurine Metabolism
- Trans-sulfuration pathway
- One carbon metabolism and related pathways
- taurine biosynthesis
Biological Process
- L-cysteine catabolic process to hypotaurine
- L-cysteine catabolic process to taurine
- taurine biosynthetic process
Molecular Function
- aspartate 1-decarboxylase activity
- sulfinoalanine decarboxylase activity
- pyridoxal phosphate binding
Cellular Component
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000267085
- Coding exons
- 16
- Length
- 23689
- Individuals with no LoFs
- 125572
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 176
- Defined
- 125748
- p
- 0.000700
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.384 | 299 | 318 | 0.939 | 0.0000196 | 3346 |
| Missense (PolyPhen) | 115 | 140.49 | 0.81858 | 1550 | ||
| Synonymous | 1.46 | 107 | 128 | 0.835 | 0.00000739 | 1060 |
| Loss of Function | 1.47 | 22 | 30.8 | 0.714 | 0.00000140 | 344 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0014 | 0.0014 | notable |
| Latino/Admixed American | 0.00087 | 0.00087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00080 | 0.00080 | rare |
| South Asian | 0.00065 | 0.00065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the decarboxylation of L-aspartate, 3-sulfino- L-alanine (cysteine sulfinic acid), and L-cysteate to beta- alanine, hypotaurine and taurine, respectively. The preferred substrate is 3-sulfino-L-alanine. Does not exhibit any decarboxylation activity toward glutamate. {ECO:0000250|UniProtKB:Q9DBE0}.;
Recessive Scores
- pRec
- 0.260
Intolerance Scores
- LoFtool
- 0.879
- RVIS EVS
- -0.33
- RVIS percentile EVS
- 30.7
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.471
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |