CYTH1
Basic information
Region (hg38): 17:78674048-78782297
Previous symbols: [ "PSCD1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (32 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYTH1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004762.6. 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 | 32 | 32 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 33 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CYTH1 | protein_coding | protein_coding | ENST00000361101 | 13 | 108250 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000190 | 125587 | 0 | 2 | 125589 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 131 | 237 | 0.554 | 0.0000143 | 2657 |
| Missense in Polyphen | 25 | 69.095 | 0.36182 | 767 | ||
| Synonymous | -0.512 | 96 | 89.8 | 1.07 | 0.00000563 | 695 |
| Loss of Function | 4.58 | 0 | 24.5 | 0.00 | 0.00000137 | 274 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| 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, ARF5 and ARF6. Promotes the activation of ARF factors through replacement of GDP with GTP. Plays an important role in membrane trafficking, during junctional remodeling and epithelial polarization, through regulation of ARF6 activity. {ECO:0000250|UniProtKB:Q9QX11, ECO:0000269|PubMed:10652308, ECO:0000269|PubMed:29420262, ECO:0000269|PubMed:9653114}.;
- Pathway
- Endocytosis - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Vesicle-mediated transport;thrombin signaling and protease-activated receptors;Membrane Trafficking;adp-ribosylation factor;Class I PI3K signaling events;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.216
Intolerance Scores
- loftool
- 0.380
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.54
Haploinsufficiency Scores
- pHI
- 0.231
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.856
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cyth1
- 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);
Gene ontology
- Biological process
- vesicle-mediated transport;regulation of cell adhesion;regulation of ARF protein signal transduction;establishment of epithelial cell polarity
- Cellular component
- Golgi membrane;cytoplasm;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;lipid binding