FCHO2
FCH and mu domain containing endocytic adaptor 2, the group of F-BAR domain containing
Basic information
Region (hg38): 5:72956041-73090522
Links
Phenotypes
GenCC
Source:
No genCC data.
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 FCHO2 gene is commonly pathogenic or not.
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 | 2 | |||||
| missense | 27 | 27 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 27 | 1 | 1 |
Variants in FCHO2
This is a list of pathogenic ClinVar variants found in the FCHO2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-72989431-A-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 5-72989496-A-C | not specified | Uncertain significance (Dec 10, 2024) | ||
| 5-72990505-C-G | not specified | Uncertain significance (Oct 16, 2024) | ||
| 5-72990597-A-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 5-73006523-G-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 5-73006534-G-A | not specified | Uncertain significance (Jan 10, 2022) | ||
| 5-73015711-T-G | not specified | Uncertain significance (Oct 27, 2023) | ||
| 5-73015716-A-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 5-73017229-A-G | not specified | Uncertain significance (May 03, 2023) | ||
| 5-73017237-T-C | not specified | Uncertain significance (May 04, 2023) | ||
| 5-73037178-C-T | not specified | Uncertain significance (May 26, 2024) | ||
| 5-73037183-A-G | Benign/Likely benign (Sep 01, 2023) | |||
| 5-73037203-A-T | not specified | Uncertain significance (Nov 03, 2022) | ||
| 5-73051352-A-G | not specified | Uncertain significance (Jun 05, 2024) | ||
| 5-73051352-A-T | not specified | Uncertain significance (Oct 25, 2023) | ||
| 5-73052335-C-A | not specified | Uncertain significance (Nov 26, 2024) | ||
| 5-73052382-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
| 5-73052401-G-A | not specified | Uncertain significance (Oct 08, 2024) | ||
| 5-73054531-A-G | not specified | Uncertain significance (May 02, 2024) | ||
| 5-73054537-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 5-73056105-T-A | not specified | Uncertain significance (Apr 12, 2024) | ||
| 5-73058492-C-A | not specified | Uncertain significance (Jun 07, 2024) | ||
| 5-73063852-A-G | not specified | Uncertain significance (Apr 20, 2023) | ||
| 5-73063916-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 5-73068681-A-G | not specified | Uncertain significance (Dec 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FCHO2 | protein_coding | protein_coding | ENST00000430046 | 26 | 134542 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000266 | 124622 | 0 | 7 | 124629 | 0.0000281 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.02 | 251 | 359 | 0.700 | 0.0000169 | 5199 |
| Missense in Polyphen | 62 | 107.01 | 0.5794 | 1491 | ||
| Synonymous | 1.41 | 103 | 123 | 0.838 | 0.00000578 | 1489 |
| Loss of Function | 5.37 | 4 | 41.2 | 0.0971 | 0.00000191 | 632 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000343 | 0.0000343 |
| Ashkenazi Jewish | 0.000108 | 0.0000994 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000482 | 0.0000464 |
| European (Non-Finnish) | 0.0000188 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000725 | 0.0000654 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in an early step of clathrin-mediated endocytosis. Has both a membrane binding/bending activity and the ability to recruit proteins essential to the formation of functional clathrin-coated pits. Has a lipid-binding activity with a preference for membranes enriched in phosphatidylserine and phosphoinositides (Pi(4,5) biphosphate) like the plasma membrane. Its membrane-bending activity might be important for the subsequent action of clathrin and adaptors in the formation of clathrin-coated vesicles. Involved in adaptor protein complex AP- 2-dependent endocytosis of the transferrin receptor, it also functions in the AP-2-independent endocytosis of the LDL receptor. {ECO:0000269|PubMed:17540576, ECO:0000269|PubMed:20448150, ECO:0000269|PubMed:21762413, ECO:0000269|PubMed:22323290}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.0988
Intolerance Scores
- loftool
- 0.328
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.85
Haploinsufficiency Scores
- pHI
- 0.709
- hipred
- Y
- hipred_score
- 0.824
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.229
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fcho2
- Phenotype
Zebrafish Information Network
- Gene name
- fcho2
- Affected structure
- ventral fin fold
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- membrane invagination;clathrin coat assembly;synaptic vesicle endocytosis;membrane organization;clathrin-dependent endocytosis;protein localization to plasma membrane;plasma membrane tubulation
- Cellular component
- cytoplasm;cytosol;cytoskeleton;plasma membrane;clathrin-coated pit;AP-2 adaptor complex;clathrin-coated vesicle;presynaptic endocytic zone membrane
- Molecular function
- phosphatidylserine binding;protein binding;phospholipid binding;phosphatidylinositol-4,5-bisphosphate binding;microtubule binding;cytoskeletal protein binding;tubulin binding;phosphatidylinositol binding;identical protein binding