GeneBe

WDFY2

WD repeat and FYVE domain containing 2, the group of WD repeat domain containing|Zinc fingers FYVE-type

Basic information

Region (hg38): 13:51584455-51767709

Links

ENSG00000139668 ∙ NCBI:115825 ∙ OMIM:610418 ∙ HGNC:20482 ∙ Uniprot:Q96P53 ∙ 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 WDFY2 gene.

  • not_specified (49 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDFY2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052950.4. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
49
clinvar
 49
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 49 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
WDFY2protein_codingprotein_codingENST00000298125 12177528
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.52e-80.8361256900581257480.000231
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.041912360.8100.00001302636
Missense in Polyphen77101.280.760241149
Synonymous-0.6659688.11.090.00000499738
Loss of Function1.581624.40.6550.00000112282

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004490.000449
Ashkenazi Jewish0.0002070.000198
East Asian0.00005480.0000544
Finnish0.0001390.000139
European (Non-Finnish)0.0001420.000141
Middle Eastern0.00005480.0000544
South Asian0.0008270.000817
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts in an adapter protein-like fashion to mediate the interaction between the kinase PRKCZ and its substrate VAMP2 and increases the PRKCZ-dependent phosphorylation of VAMP2 (PubMed:17313651). Positively regulates adipocyte differentiation, by facilitating the phosphorylation and thus inactivation of the anti-adipogenetic transcription factor FOXO1 by the kinase AKT1 (PubMed:18388859). Plays a role in endosomal control of AKT2 signaling; required for insulin-stimulated AKT2 phosphorylation and glucose uptake and insulin-stimulated phosphorylation of AKT2 substrates (By similarity). Participates in transferrin receptor endocytosis (PubMed:16873553). {ECO:0000250|UniProtKB:Q8BUB4, ECO:0000269|PubMed:16873553, ECO:0000269|PubMed:17313651, ECO:0000269|PubMed:18388859}.;
Pathway
Mesodermal Commitment Pathway (Consensus)

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
0.806
rvis_EVS
-0.05
rvis_percentile_EVS
50.22

Haploinsufficiency Scores

pHI
0.170
hipred
Y
hipred_score
0.756
ghis
0.492

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0941

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Wdfy2
Phenotype

Gene ontology

Biological process
positive regulation of protein phosphorylation;positive regulation of fat cell differentiation
Cellular component
early endosome;vesicle
Molecular function
protein binding;metal ion binding