CAP2
protein-codingcyclase associated actin cytoskeleton regulatory protein 2
Gene summary
This gene was identified by its similarity to the gene for human adenylyl cyclase-associated protein. The function of the protein encoded by this gene is unknown. However, the protein appears to be able to interact with adenylyl cyclase-associated protein and actin. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~164.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015470
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0957545
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal
Intervention: Cardiovascular
Rationale: The condition can involve structural cardiac anomalies, arrhthymias, and congestive heart failure, and awanress may be beneficial realed to medical management; Cardiac transplant has been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CAP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006366.3. 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 | ||||
| missense | 71 | 3 | 74 | |||
| nonsense | 1 | 1 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 2 | |||
| Total | 3 | 1 | 75 | 3 | 0 | 82 |
Highest pathogenic variant AF is 0.0000068271843
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006357.1 | 12 | MANE Select | |
| Ensembl | ENSP00000229922.2 | 12 | MANE Select | |
| RefSeq | NP_001350462.1 | 9 | Standard | |
| RefSeq | NP_001350463.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cap2 | Danio rerio | Structure: whole organism Quality: decreased length abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ectoderm Differentiation
- Aryl Hydrocarbon Receptor Pathway
- Nuclear Receptors Meta-Pathway
- Developmental Biology
- Signaling by ROBO receptors
Biological Process
- cell morphogenesis
- establishment or maintenance of cell polarity
- signal transduction
- activation of adenylate cyclase activity
- actin polymerization or depolymerization
Molecular Function
- actin binding
- protein binding
- adenylate cyclase binding
- identical protein binding
Cellular Component
- plasma membrane
- postsynaptic density
- cortical actin cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000229922
- Coding exons
- 12
- Length
- 164577
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125746
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.10 | 221 | 272 | 0.812 | 0.0000145 | 3141 |
| Missense (PolyPhen) | 77 | 119.43 | 0.64474 | 1408 | ||
| Synonymous | 0.532 | 93 | 99.8 | 0.932 | 0.00000589 | 906 |
| Loss of Function | 3.80 | 5 | 25.9 | 0.193 | 0.00000119 | 305 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May have a regulatory bifunctional role.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.312
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 50.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0194
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |