PENK
Basic information
Region (hg38): 8:56436674-56446671
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (38 variants)
- not_provided (9 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PENK gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135690.3. 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 | 6 | |||||
missense | 36 | 40 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 36 | 5 | 5 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PENK | protein_coding | protein_coding | ENST00000314922 | 2 | 10061 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000208 | 0.747 | 125653 | 0 | 95 | 125748 | 0.000378 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.725 | 179 | 154 | 1.16 | 0.00000853 | 1756 |
Missense in Polyphen | 57 | 50.235 | 1.1347 | 558 | ||
Synonymous | 0.400 | 58 | 62.0 | 0.935 | 0.00000346 | 498 |
Loss of Function | 1.01 | 7 | 10.5 | 0.665 | 6.25e-7 | 123 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00133 | 0.00133 |
Ashkenazi Jewish | 0.00218 | 0.00218 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.000247 | 0.000246 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000294 | 0.000294 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Met- and Leu-enkephalins compete with and mimic the effects of opiate drugs. They play a role in a number of physiologic functions, including pain perception and responses to stress. PENK(114-133) and PENK(237-258) increase glutamate release in the striatum. PENK(114-133) decreases GABA concentration in the striatum.;
- Pathway
- Signaling by GPCR;Signal Transduction;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);G alpha (i) signalling events;GPCR downstream signalling;AP-1 transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.375
Intolerance Scores
- loftool
- 0.826
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.6
Haploinsufficiency Scores
- pHI
- 0.182
- hipred
- N
- hipred_score
- 0.342
- ghis
- 0.422
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.506
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Penk
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal 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); reproductive system phenotype; limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- osteoblast differentiation;behavioral fear response;response to hypoxia;startle response;aggressive behavior;signal transduction;G protein-coupled receptor signaling pathway;neuropeptide signaling pathway;chemical synaptic transmission;aging;response to radiation;regulation of signaling receptor activity;glial cell proliferation;sensory perception of pain;response to estradiol;response to lipopolysaccharide;cellular response to oxidative stress;response to nicotine;locomotory exploration behavior;response to morphine;post-translational protein modification;cellular protein metabolic process;response to ethanol;response to calcium ion;general adaptation syndrome, behavioral process;cellular response to vitamin D;cellular response to cAMP;cellular response to transforming growth factor beta stimulus;response to epinephrine;cellular response to virus;positive regulation of behavioral fear response
- Cellular component
- extracellular region;endoplasmic reticulum lumen;plasma membrane;dendrite;symmetric synapse;synaptic vesicle lumen;neuronal cell body;perikaryon;axon terminus;cell body fiber;neuronal dense core vesicle lumen
- Molecular function
- opioid peptide activity;neuropeptide hormone activity;opioid receptor binding