CPNE1
Basic information
Region (hg38): 20:35626031-35664956
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (178 variants)
- not_provided (9 variants)
- RBM12-related_disorder (6 variants)
- Schizophrenia_19 (5 variants)
- Neurodevelopmental_delay (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152925.3. 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 | 73 | 77 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 73 | 6 | 0 |
Highest pathogenic variant AF is 0.0000013723464
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CPNE1 | protein_coding | protein_coding | ENST00000317677 | 16 | 38926 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.73e-14 | 0.185 | 100225 | 1579 | 23944 | 125748 | 0.107 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0942 | 316 | 321 | 0.985 | 0.0000193 | 3521 |
| Missense in Polyphen | 116 | 117.48 | 0.98737 | 1442 | ||
| Synonymous | 1.12 | 106 | 122 | 0.871 | 0.00000689 | 1079 |
| Loss of Function | 1.08 | 25 | 31.6 | 0.792 | 0.00000156 | 349 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.201 | 0.201 |
| Ashkenazi Jewish | 0.141 | 0.139 |
| East Asian | 0.0829 | 0.0823 |
| Finnish | 0.0734 | 0.0735 |
| European (Non-Finnish) | 0.106 | 0.104 |
| Middle Eastern | 0.0829 | 0.0823 |
| South Asian | 0.159 | 0.157 |
| Other | 0.116 | 0.114 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes (PubMed:14674885). Involved in the TNF-alpha receptor signaling pathway in a calcium-dependent manner (PubMed:14674885). Exhibits calcium-dependent phospholipid binding properties (PubMed:9430674, PubMed:19539605). Plays a role in neuronal progenitor cell differentiation; induces neurite outgrowth via a AKT-dependent signaling cascade and calcium-independent manner (PubMed:23263657, PubMed:25450385). May recruit target proteins to the cell membrane in a calcium-dependent manner (PubMed:12522145). May function in membrane trafficking (PubMed:9430674). Involved in TNF-alpha- induced NF-kappa-B transcriptional repression by inducing endoprotease processing of the transcription factor NF-kappa-B p65/RELA subunit (PubMed:18212740). Also induces endoprotease processing of NF-kappa-B p50/NFKB1, p52/NFKB2, RELB and REL (PubMed:18212740). {ECO:0000269|PubMed:12522145, ECO:0000269|PubMed:14674885, ECO:0000269|PubMed:18212740, ECO:0000269|PubMed:19539605, ECO:0000269|PubMed:23263657, ECO:0000269|PubMed:25450385, ECO:0000269|PubMed:9430674}.;
- Pathway
- Neutrophil degranulation;Metabolism of lipids;Innate Immune System;Immune System;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.866
- rvis_EVS
- 1
- rvis_percentile_EVS
- 90.72
Haploinsufficiency Scores
- pHI
- 0.112
- hipred
- N
- hipred_score
- 0.229
- ghis
- 0.487
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.875
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Cpne1
- Phenotype
Gene ontology
- Biological process
- proteolysis;lipid metabolic process;negative regulation of gene expression;vesicle-mediated transport;regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation;negative regulation of DNA binding;positive regulation of neuron differentiation;glycerophospholipid biosynthetic process;positive regulation of protein kinase B signaling;cellular response to calcium ion;negative regulation of NIK/NF-kappaB signaling;positive regulation of tumor necrosis factor-mediated signaling pathway;neuron projection extension
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;membrane;nuclear membrane;azurophil granule membrane;extracellular exosome
- Molecular function
- phosphatidylserine binding;endopeptidase activity;transporter activity;calcium ion binding;protein binding;calcium-dependent phospholipid binding;protein homodimerization activity;NF-kappaB binding