CALY
protein-codingcalcyon neuron specific vesicular protein
Gene summary
The protein encoded by this gene is a type II single transmembrane protein. It is required for maximal stimulated calcium release after stimulation of purinergic or muscarinic but not beta-adrenergic receptors. The encoded protein interacts with D1 dopamine receptor and may interact with other DA receptor subtypes and/or GPCRs. [provided by RefSeq, Jul 2008]
- DRD1IP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.9 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 CALY variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015722.4. 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 | 1 | 1 | ||||
| missense | 31 | 31 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 31 | 1 | 0 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056537.1 | 4 | MANE Select | |
| Ensembl | ENSP00000252939.4 | 4 | MANE Select | |
| RefSeq | NP_001308546.1 | 1 | Standard | |
| Ensembl | ENSP00000357543.3 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Dopaminergic synapse - Homo sapiens (human)
Biological Process
- dopamine receptor signaling pathway
- endosomal transport
- positive regulation of endocytosis
- clathrin coat assembly
- postsynaptic neurotransmitter receptor internalization
Molecular Function
- protein binding
- clathrin light chain binding
- cargo receptor activity
- protein-containing complex binding
Cellular Component
- endosome
- integral component of plasma membrane
- cytoplasmic vesicle membrane
- cytoplasmic vesicle
- postsynaptic endocytic zone
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000252939
- Coding exons
- 4
- Length
- 11549
- Individuals with no LoFs
- 124728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 124731
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.26 | 67 | 103 | 0.650 | 0.00000548 | 1375 |
| Missense (PolyPhen) | 20 | 41.572 | 0.4811 | 489 | ||
| Synonymous | 0.318 | 41 | 43.7 | 0.939 | 0.00000239 | 439 |
| Loss of Function | 1.28 | 3 | 6.52 | 0.460 | 2.78e-7 | 75 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.00011 | 0.00010 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Interacts with clathrin light chain A and stimulates clathrin self-assembly and clathrin-mediated endocytosis. {ECO:0000269|PubMed:16595675}.;
Recessive Scores
- pRec
- 0.131
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.245
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |