FCHO2

FCH and mu domain containing endocytic adaptor 2, the group of F-BAR domain containing

Basic information

Region (hg38): 5:72956041-73090522

Links

ENSG00000157107

∙ NCBI:115548 ∙ OMIM:613438 ∙ HGNC:25180 ∙ Uniprot:Q0JRZ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FCHO2 gene.

not_specified (72 variants)
not_provided (2 variants)

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. These statistics are base on transcript: NM_000138782.3. 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				1 clinvar	1 clinvar	2
missense			72 clinvar			72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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