CYTH3
Basic information
Region (hg38): 7:6161779-6272644
Previous symbols: [ "PSCD3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (29 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTH3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004227.4. 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 | 0 | |||||
| missense | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 29 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CYTH3 | protein_coding | protein_coding | ENST00000350796 | 13 | 110869 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.723 | 0.277 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.57 | 133 | 247 | 0.539 | 0.0000155 | 2662 |
| Missense in Polyphen | 36 | 102.01 | 0.35292 | 1103 | ||
| Synonymous | -2.15 | 127 | 99.6 | 1.27 | 0.00000714 | 701 |
| Loss of Function | 3.53 | 4 | 21.7 | 0.184 | 9.65e-7 | 279 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000185 | 0.000185 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Play a role in the epithelial polarization (By similarity). {ECO:0000250|UniProtKB:O08967, ECO:0000269|PubMed:23940353, ECO:0000269|PubMed:9707577}.;
- Pathway
- Endocytosis - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Insulin Signaling;Vesicle-mediated transport;thrombin signaling and protease-activated receptors;Membrane Trafficking;adp-ribosylation factor;Class I PI3K signaling events;Intra-Golgi traffic;Arf6 signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.146
Intolerance Scores
- loftool
- 0.424
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.26
Haploinsufficiency Scores
- pHI
- 0.128
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.637
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.787
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cyth3
- Phenotype
Gene ontology
- Biological process
- regulation of ARF protein signal transduction;positive regulation of cell adhesion;Golgi vesicle transport;establishment of epithelial cell polarity
- Cellular component
- Golgi membrane;ruffle;nucleoplasm;cytosol;plasma membrane;adherens junction;bicellular tight junction;extrinsic component of cytoplasmic side of plasma membrane
- Molecular function
- ARF guanyl-nucleotide exchange factor activity;protein binding;phosphatidylinositol-3,4,5-trisphosphate binding