PACSIN2
protein kinase C and casein kinase substrate in neurons 2, the group of F-BAR domain containing
Basic information
Region (hg38): 22:42835412-43015149
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (45 variants)
- not_provided (1 variants)
- Myoepithelial_tumor (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PACSIN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001184970.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 48 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 50 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PACSIN2 | protein_coding | protein_coding | ENST00000263246 | 10 | 179734 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.213 | 0.787 | 125717 | 0 | 23 | 125740 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.30 | 248 | 313 | 0.793 | 0.0000202 | 3243 |
| Missense in Polyphen | 86 | 120.78 | 0.71205 | 1249 | ||
| Synonymous | -0.346 | 140 | 135 | 1.04 | 0.0000101 | 853 |
| Loss of Function | 3.78 | 7 | 28.9 | 0.242 | 0.00000157 | 299 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000111 | 0.000109 |
| Finnish | 0.000509 | 0.000508 |
| European (Non-Finnish) | 0.0000709 | 0.0000703 |
| Middle Eastern | 0.000111 | 0.000109 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000165 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Lipid-binding protein that is able to promote the tubulation of the phosphatidic acid-containing membranes it preferentially binds. Plays a role in intracellular vesicle- mediated transport. Involved in the endocytosis of cell-surface receptors like the EGF receptor, contributing to its internalization in the absence of EGF stimulus. May also play a role in the formation of caveolae at the cell membrane. Recruits DNM2 to caveolae, and thereby plays a role in caveola-mediated endocytosis. {ECO:0000269|PubMed:21610094, ECO:0000269|PubMed:21693584, ECO:0000269|PubMed:23129763, ECO:0000269|PubMed:23236520, ECO:0000269|PubMed:23596323}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.207
Intolerance Scores
- loftool
- 0.405
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 57.41
Haploinsufficiency Scores
- pHI
- 0.248
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.446
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.736
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pacsin2
- Phenotype
- homeostasis/metabolism phenotype; hearing/vestibular/ear phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- cytoskeleton organization;actin cytoskeleton organization;protein localization to endosome;negative regulation of endocytosis;cell projection morphogenesis;modulation of chemical synaptic transmission;membrane organization;caveola assembly;caveolin-mediated endocytosis;plasma membrane tubulation
- Cellular component
- cytoplasm;early endosome;cytosol;cytoskeleton;plasma membrane;caveola;cell-cell junction;focal adhesion;nuclear speck;extrinsic component of membrane;cytoplasmic vesicle membrane;ruffle membrane;intracellular membrane-bounded organelle;recycling endosome membrane;extracellular exosome;glutamatergic synapse
- Molecular function
- transporter activity;protein binding;phospholipid binding;cytoskeletal protein binding;identical protein binding;cadherin binding;phosphatidic acid binding