ZFYVE9
Basic information
Region (hg38): 1:52142089-52348671
Previous symbols: [ "MADHIP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFYVE9 gene is commonly pathogenic or not. These statistics are base on transcript: . 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 97 | 102 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 97 | 5 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ZFYVE9 | protein_coding | protein_coding | ENST00000287727 | 17 | 204313 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.902 | 0.0976 | 125732 | 0 | 14 | 125746 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.80 | 604 | 742 | 0.814 | 0.0000358 | 9455 |
| Missense in Polyphen | 162 | 295.91 | 0.54746 | 3833 | ||
| Synonymous | 0.850 | 254 | 272 | 0.934 | 0.0000140 | 2688 |
| Loss of Function | 5.57 | 11 | 56.0 | 0.196 | 0.00000266 | 746 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000918 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000713 | 0.0000703 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000986 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Early endosomal protein that functions to recruit SMAD2/SMAD3 to intracellular membranes and to the TGF-beta receptor. Plays a significant role in TGF-mediated signaling by regulating the subcellular location of SMAD2 and SMAD3 and modulating the transcriptional activity of the SMAD3/SMAD4 complex. Possibly associated with TGF-beta receptor internalization. {ECO:0000269|PubMed:15356634, ECO:0000269|PubMed:9865696}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);TGF-Ncore;TGF-beta Signaling Pathway;TGF-beta Receptor Signaling;Disease;Signal Transduction;TGF_beta_Receptor;SMAD2/3 Phosphorylation Motif Mutants in Cancer;SMAD2/3 MH2 Domain Mutants in Cancer;Loss of Function of SMAD2/3 in Cancer;Signaling by TGF-beta Receptor Complex in Cancer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Downregulation of TGF-beta receptor signaling;TGF-beta receptor signaling activates SMADs;Diseases of signal transduction;TGF-beta receptor signaling
(Consensus)
Intolerance Scores
- loftool
- 0.532
- rvis_EVS
- 0.14
- rvis_percentile_EVS
- 63.65
Haploinsufficiency Scores
- pHI
- 0.562
- hipred
- N
- hipred_score
- 0.493
- ghis
- 0.512
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.962
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Zfyve9
- Phenotype
Zebrafish Information Network
- Gene name
- zfyve9a
- Affected structure
- spinal cord
- Phenotype tag
- abnormal
- Phenotype quality
- process quality
Gene ontology
- Biological process
- proteolysis;endocytosis;transforming growth factor beta receptor signaling pathway;endosomal transport
- Cellular component
- early endosome;cytosol;early endosome membrane;protein-containing complex;intracellular membrane-bounded organelle
- Molecular function
- protein binding;1-phosphatidylinositol binding;serine-type peptidase activity;protein domain specific binding;metal ion binding