PICK1
Basic information
Region (hg38): 22:38056311-38075701
Previous symbols: [ "PRKCABP" ]
Links
Phenotypes
GenCC
Source:
- male infertility due to globozoospermia (Supportive), mode of inheritance: AR
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 PICK1 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 | 1 | |||||
missense | 15 | 15 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 1 | |||||
Total | 0 | 0 | 15 | 0 | 2 |
Variants in PICK1
This is a list of pathogenic ClinVar variants found in the PICK1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-38057829-A-G | not specified | Uncertain significance (Jun 29, 2022) | ||
22-38065032-G-A | not specified | Uncertain significance (Nov 25, 2024) | ||
22-38065062-G-C | not specified | Uncertain significance (Oct 29, 2021) | ||
22-38065125-G-A | not specified | Uncertain significance (Jun 04, 2024) | ||
22-38069027-G-A | PICK1-related disorder | Benign (Sep 12, 2018) | ||
22-38069083-G-A | not specified | Uncertain significance (Apr 26, 2023) | ||
22-38071734-G-C | not specified | Uncertain significance (Aug 01, 2024) | ||
22-38071738-C-G | not specified | Uncertain significance (Jan 08, 2024) | ||
22-38071742-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
22-38072497-G-A | not specified | Uncertain significance (Jul 25, 2023) | ||
22-38072522-C-G | not specified | Uncertain significance (Oct 03, 2023) | ||
22-38073028-A-G | not specified | Uncertain significance (Mar 01, 2023) | ||
22-38073806-G-A | not specified | Uncertain significance (Aug 17, 2022) | ||
22-38074340-G-A | not specified | Uncertain significance (Dec 19, 2023) | ||
22-38074345-C-G | not specified | Uncertain significance (Apr 15, 2024) | ||
22-38074449-A-G | not specified | Uncertain significance (Oct 17, 2023) | ||
22-38074931-C-T | Benign (Mar 30, 2018) | |||
22-38074932-G-A | not specified | Uncertain significance (Aug 28, 2023) | ||
22-38075025-G-A | not specified | Uncertain significance (Aug 17, 2022) | ||
22-38075035-A-G | not specified | Uncertain significance (Jan 04, 2022) | ||
22-38075083-G-A | not specified | Uncertain significance (Oct 20, 2023) | ||
22-38075140-G-A | PICK1-related disorder | Benign (Jun 10, 2019) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PICK1 | protein_coding | protein_coding | ENST00000404072 | 12 | 19391 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00818 | 0.989 | 125451 | 0 | 295 | 125746 | 0.00117 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.01 | 172 | 264 | 0.651 | 0.0000186 | 2703 |
Missense in Polyphen | 53 | 97.808 | 0.54188 | 962 | ||
Synonymous | -0.0573 | 110 | 109 | 1.01 | 0.00000802 | 789 |
Loss of Function | 2.64 | 7 | 19.6 | 0.357 | 8.55e-7 | 252 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00434 | 0.00432 |
Ashkenazi Jewish | 0.00463 | 0.00388 |
East Asian | 0.000228 | 0.000217 |
Finnish | 0.00276 | 0.00264 |
European (Non-Finnish) | 0.000583 | 0.000554 |
Middle Eastern | 0.000228 | 0.000217 |
South Asian | 0.0000334 | 0.0000327 |
Other | 0.00143 | 0.00130 |
dbNSFP
Source:
- Function
- FUNCTION: Probable adapter protein that bind to and organize the subcellular localization of a variety of membrane proteins containing some PDZ recognition sequence. Involved in the clustering of various receptors, possibly by acting at the receptor internalization level. Plays a role in synaptic plasticity by regulating the trafficking and internalization of AMPA receptors. May be regulated upon PRKCA activation. May regulate ASIC1/ASIC3 channel. Regulates actin polymerization by inhibiting the actin-nucleating activity of the Arp2/3 complex; the function is competetive with nucleation promoting factors and is linked to neuronal morphology regulation and AMPA receptor (AMPAR) endocytosis. Via interaction with the Arp2/3 complex involved in regulation of synaptic plasicity of excitatory synapses and required for spine shrinkage during long-term depression (LTD). Involved in regulation of astrocyte morphology, antagonistic to Arp2/3 complex activator WASL/N-WASP function. {ECO:0000269|PubMed:20403402}.;
- Pathway
- Neuronal System;Cell surface interactions at the vascular wall;Hemostasis;Trafficking of GluR2-containing AMPA receptors;Trafficking of AMPA receptors;Glutamate binding, activation of AMPA receptors and synaptic plasticity;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses
(Consensus)
Recessive Scores
- pRec
- 0.270
Intolerance Scores
- loftool
- 0.397
- rvis_EVS
- -0.8
- rvis_percentile_EVS
- 12.24
Haploinsufficiency Scores
- pHI
- 0.238
- hipred
- Y
- hipred_score
- 0.785
- ghis
- 0.680
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pick1
- Phenotype
- endocrine/exocrine gland phenotype; cellular 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;
Gene ontology
- Biological process
- positive regulation of receptor internalization;protein phosphorylation;intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;protein kinase C-activating G protein-coupled receptor signaling pathway;monoamine transport;glial cell development;negative regulation of Arp2/3 complex-mediated actin nucleation;cellular response to decreased oxygen levels;cellular response to glucose starvation;DNA methylation involved in embryo development;DNA methylation involved in gamete generation;receptor clustering;neuronal ion channel clustering;long-term synaptic depression;dendritic spine organization;dendritic spine maintenance
- Cellular component
- cytoplasm;mitochondrion;Golgi apparatus;cytosol;cytoskeleton;plasma membrane;synaptic vesicle;postsynaptic density;aggresome;cell junction;endocytic vesicle membrane;trans-Golgi network membrane;presynaptic membrane;neuron projection;synapse;postsynaptic membrane;perinuclear region of cytoplasm;postsynaptic early endosome
- Molecular function
- G protein-coupled receptor binding;protein kinase C binding;signaling receptor binding;protein binding;phospholipid binding;protein C-terminus binding;enzyme binding;protein domain specific binding;identical protein binding;metal ion binding;actin filament binding;Arp2/3 complex binding