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
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.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 0 | 0 |
Variants in PACSIN1
This is a list of pathogenic ClinVar variants found in the PACSIN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-34526321-G-A | not specified | Uncertain significance (May 17, 2023) | ||
| 6-34527411-A-G | not specified | Uncertain significance (Nov 09, 2024) | ||
| 6-34528665-C-T | not specified | Uncertain significance (Mar 20, 2023) | ||
| 6-34528674-G-A | not specified | Uncertain significance (Oct 07, 2024) | ||
| 6-34528675-G-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 6-34528824-G-T | not specified | Uncertain significance (Feb 08, 2023) | ||
| 6-34528839-C-T | not specified | Uncertain significance (Apr 13, 2022) | ||
| 6-34529407-C-G | not specified | Uncertain significance (May 09, 2022) | ||
| 6-34529413-A-G | not specified | Uncertain significance (Sep 30, 2024) | ||
| 6-34529451-A-G | not specified | Uncertain significance (Feb 06, 2024) | ||
| 6-34529464-T-C | not specified | Uncertain significance (Apr 25, 2023) | ||
| 6-34529476-C-T | not specified | Uncertain significance (Dec 20, 2022) | ||
| 6-34529509-A-G | not specified | Uncertain significance (Aug 14, 2024) | ||
| 6-34529748-A-C | not specified | Uncertain significance (May 17, 2023) | ||
| 6-34529823-A-G | not specified | Uncertain significance (May 14, 2024) | ||
| 6-34530259-C-G | not specified | Uncertain significance (Jul 12, 2022) | ||
| 6-34530351-G-C | not specified | Uncertain significance (Oct 04, 2024) | ||
| 6-34530526-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 6-34530547-G-A | not specified | Uncertain significance (Aug 16, 2021) | ||
| 6-34531601-G-A | not specified | Uncertain significance (Dec 18, 2023) | ||
| 6-34531639-G-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 6-34531665-C-T | not specified | Uncertain significance (Mar 11, 2022) | ||
| 6-34531691-G-A | not specified | Uncertain significance (May 11, 2022) | ||
| 6-34531754-G-A | not specified | Uncertain significance (Nov 07, 2023) | ||
| 6-34532484-G-A | not specified | Uncertain significance (Mar 29, 2023) |
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