EXOC4
Basic information
Region (hg38): 7:133253072-134067137
Previous symbols: [ "SEC8L1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (121 variants)
- not_provided (7 variants)
- Polymerase_proofreading-related_adenomatous_polyposis (4 variants)
- Familial_colorectal_cancer_type_X (4 variants)
- Meckel-Gruber_syndrome (1 variants)
- Facial_dysmorphism-immunodeficiency-livedo-short_stature_syndrome (1 variants)
- Intrauterine_growth_retardation,_metaphyseal_dysplasia,_adrenal_hypoplasia_congenita,_genital_anomalies,_and_immunodeficiency (1 variants)
- Colorectal_cancer,_susceptibility_to,_12 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOC4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021807.4. 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 | 5 | |||||
| missense | 119 | 124 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 119 | 5 | 4 |
Highest pathogenic variant AF is 0.00000687068
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EXOC4 | protein_coding | protein_coding | ENST00000253861 | 18 | 813514 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.41e-13 | 0.994 | 125683 | 0 | 65 | 125748 | 0.000258 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.516 | 505 | 539 | 0.937 | 0.0000291 | 6431 |
| Missense in Polyphen | 124 | 153.95 | 0.80544 | 1945 | ||
| Synonymous | -0.162 | 210 | 207 | 1.01 | 0.0000115 | 1864 |
| Loss of Function | 2.70 | 28 | 48.3 | 0.580 | 0.00000267 | 559 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000729 | 0.000728 |
| Ashkenazi Jewish | 0.000210 | 0.000198 |
| East Asian | 0.000219 | 0.000217 |
| Finnish | 0.0000939 | 0.0000924 |
| European (Non-Finnish) | 0.000292 | 0.000290 |
| Middle Eastern | 0.000219 | 0.000217 |
| South Asian | 0.000300 | 0.000294 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane. {ECO:0000250}.;
- Pathway
- Arf6 trafficking events;VxPx cargo-targeting to cilium;Stabilization and expansion of the E-cadherin adherens junction;Insulin Pathway;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Intolerance Scores
- loftool
- 0.0710
- rvis_EVS
- -1.28
- rvis_percentile_EVS
- 5.17
Haploinsufficiency Scores
- pHI
- 0.459
- hipred
- Y
- hipred_score
- 0.578
- ghis
- 0.605
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Exoc4
- Phenotype
- hearing/vestibular/ear 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); embryo phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- protein targeting to membrane;exocytosis;Golgi to plasma membrane transport;vesicle docking involved in exocytosis;chemical synaptic transmission;regulation of macroautophagy;paraxial mesoderm formation;vesicle tethering involved in exocytosis
- Cellular component
- exocyst;cytoplasm;cytosol;plasma membrane;microvillus;membrane;growth cone membrane;myelin sheath abaxonal region;synapse;Flemming body
- Molecular function
- protein binding;Ral GTPase binding;PDZ domain binding;protein N-terminus binding