WDFY2

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

Basic information

Region (hg38): 13:51584454-51767709

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.

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.

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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in WDFY2

This is a list of pathogenic ClinVar variants found in the WDFY2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-51584725-A-G		not specified	Uncertain significance (Jun 17, 2024)
13-51584745-A-T		not specified	Uncertain significance (Jun 03, 2022)
13-51584755-C-T		not specified	Uncertain significance (May 15, 2024)
13-51584810-C-A		not specified	Uncertain significance (Feb 17, 2023)
13-51584815-C-T		not specified	Uncertain significance (May 22, 2023)
13-51660604-G-A		not specified	Uncertain significance (Jul 16, 2021)
13-51660621-G-C		not specified	Uncertain significance (Sep 01, 2021)
13-51660643-G-A		not specified	Uncertain significance (Jul 06, 2022)
13-51675188-C-G		not specified	Uncertain significance (Dec 06, 2021)
13-51675193-A-G		not specified	Uncertain significance (May 26, 2022)
13-51719231-T-C		not specified	Uncertain significance (May 29, 2024)
13-51719321-G-A		not specified	Uncertain significance (Jan 23, 2024)
13-51727695-G-A		not specified	Uncertain significance (Aug 04, 2021)
13-51727772-A-G		not specified	Uncertain significance (Oct 26, 2022)
13-51739060-G-A		not specified	Uncertain significance (May 30, 2024)
13-51739159-G-A		not specified	Uncertain significance (May 31, 2023)
13-51751386-G-A		not specified	Uncertain significance (May 26, 2024)
13-51751406-G-C		not specified	Uncertain significance (Jun 13, 2024)
13-51756339-G-A		not specified	Uncertain significance (Mar 18, 2024)
13-51756359-G-A		not specified	Uncertain significance (Jul 09, 2021)
13-51756402-T-A		not specified	Uncertain significance (Aug 13, 2021)
13-51756443-G-A		not specified	Uncertain significance (Feb 15, 2023)
13-51758267-G-C		not specified	Uncertain significance (Oct 10, 2023)
13-51758278-C-G		not specified	Uncertain significance (May 26, 2023)
13-51758292-G-T		not specified	Uncertain significance (Oct 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDFY2	protein_coding	protein_coding	ENST00000298125	12	177528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-8	0.836	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	191	236	0.810	0.0000130	2636
Missense in Polyphen		77	101.28	0.76024		1149
Synonymous	-0.665	96	88.1	1.09	0.00000499	738
Loss of Function	1.58	16	24.4	0.655	0.00000112	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000449
Ashkenazi Jewish	0.000207	0.000198
East Asian	0.0000548	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000548	0.0000544
South Asian	0.000827	0.000817
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Wdfy2

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