PACSIN1
protein kinase C and casein kinase substrate in neurons 1, the group of F-BAR domain containing
Basic information
Region (hg38): 6:34466061-34535229
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PACSIN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020804.5. 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 | 0 | |||||
| missense | 34 | 34 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PACSIN1 | protein_coding | protein_coding | ENST00000538621 | 9 | 69091 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.00113 | 125707 | 0 | 3 | 125710 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.63 | 140 | 259 | 0.540 | 0.0000151 | 2936 |
| Missense in Polyphen | 29 | 78.896 | 0.36757 | 901 | ||
| Synonymous | 1.10 | 89 | 103 | 0.862 | 0.00000669 | 770 |
| Loss of Function | 4.36 | 1 | 24.1 | 0.0415 | 0.00000103 | 285 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000906 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the reorganization of the microtubule cytoskeleton via its interaction with MAPT; this decreases microtubule stability and inhibits MAPT-induced microtubule polymerization. Plays a role in cellular transport processes by recruiting DNM1, DNM2 and DNM3 to membranes. Plays a role in the reorganization of the actin cytoskeleton and in neuron morphogenesis via its interaction with COBL and WASL, and by recruiting COBL to the cell cortex. Plays a role in the regulation of neurite formation, neurite branching and the regulation of neurite length. Required for normal synaptic vesicle endocytosis; this process retrieves previously released neurotransmitters to accommodate multiple cycles of neurotransmission. Required for normal excitatory and inhibitory synaptic transmission (By similarity). Binds to membranes via its F-BAR domain and mediates membrane tubulation. {ECO:0000250, ECO:0000269|PubMed:19549836, ECO:0000269|PubMed:22573331, ECO:0000269|PubMed:23236520}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.207
Intolerance Scores
- loftool
- 0.0814
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.57
Haploinsufficiency Scores
- pHI
- 0.298
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.968
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pacsin1
- Phenotype
- immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- pacsin1b
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- cytoskeleton organization;actin filament organization;synaptic vesicle endocytosis;neuron projection morphogenesis;protein localization to membrane;protein localization to plasma membrane;plasma membrane tubulation;positive regulation of dendrite development
- Cellular component
- cytoplasm;cytosol;cytoskeleton;plasma membrane;cell junction;cytoplasmic vesicle membrane;ruffle membrane;axon terminus;synapse;perinuclear region of cytoplasm
- Molecular function
- protein binding;phospholipid binding;cytoskeletal protein binding