CARNS1
protein-codingcarnosine synthase 1
Gene summary
CARNS1 (EC 6.3.2.11), a member of the ATP-grasp family of ATPases, catalyzes the formation of carnosine (beta-alanyl-L-histidine) and homocarnosine (gamma-aminobutyryl-L-histidine), which are found mainly in skeletal muscle and the central nervous system, respectively (Drozak et al., 2010 [PubMed 20097752]).[supplied by OMIM, Apr 2010]
- ATPGD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.6 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 CARNS1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001166222.2. 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 | 177 | 7 | 184 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 178 | 7 | 0 | 185 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001159694.1 | 9 | MANE Select | |
| Ensembl | ENSP00000510668.1 | 9 | MANE Select | |
| RefSeq | NP_001381506.1 | 8 | Standard | |
| RefSeq | NP_001381507.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Arginine and proline metabolism - Homo sapiens (human)
- beta-Alanine metabolism - Homo sapiens (human)
- Histidine metabolism - Homo sapiens (human)
- Histidine Metabolism
- Histidinemia
Biological Process
- histidine catabolic process
- carnosine biosynthetic process
Molecular Function
- ATP binding
- FMN binding
- ATPase activity
- metal ion binding
- carnosine synthase activity
Cellular Component
- cellular_component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000445895
- Coding exons
- 9
- Length
- 10640
- Individuals with no LoFs
- 124599
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 61
- Defined
- 124660
- p
- 0.000245
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 397 | 459 | 0.865 | 0.0000296 | 5835 |
| Missense (PolyPhen) | 125 | 147.3 | 0.84861 | 1718 | ||
| Synonymous | 1.52 | 176 | 204 | 0.865 | 0.0000124 | 2162 |
| Loss of Function | 2.06 | 13 | 23.9 | 0.544 | 0.00000128 | 328 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000085 | 0.000064 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00065 | 0.00061 | rare |
| Finnish | 0.000051 | 0.000046 | rare |
| European (Non-Finnish) | 0.00041 | 0.00036 | rare |
| South Asian | 0.000036 | 0.000033 | rare |
| Other | 0.00037 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the synthesis of carnosine and homocarnosine. Carnosine is synthesized more efficiently than homocarnosine. {ECO:0000269|PubMed:20097752}.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |