WIPI1

WD repeat domain, phosphoinositide interacting 1, the group of WD repeat domain containing|WIPI family|Autophagy related

Basic information

Region (hg38): 17:68420948-68457513

Links

ENSG00000070540

∙ NCBI:55062 ∙ OMIM:609224 ∙ HGNC:25471 ∙ Uniprot:Q5MNZ9 ∙ 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 WIPI1 gene.

not_specified (57 variants)
not_provided (3 variants)
WIPI1-related_disorder (2 variants)
Acrodysostosis_1_with_or_without_hormone_resistance (1 variants)
Neural_tube_defect (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WIPI1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017983.7. 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			58 clinvar	1 clinvar	1 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	2	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WIPI1	protein_coding	protein_coding	ENST00000262139	13	36566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00170	0.997	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	196	255	0.768	0.0000144	2879
Missense in Polyphen		65	81.968	0.793		912
Synonymous	1.28	87	104	0.840	0.00000632	885
Loss of Function	2.86	9	24.2	0.372	0.00000127	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plays an important role in autophagy and in particular starvation- and calcium-mediated autophagy, as well as in mitophagy. Functions upstream of the ATG12-ATG5-ATG16L1 complex and LC3, and downstream of the ULK1 and PI3-kinase complexes. Involved in xenophagy of Staphylococcus aureus. Invading S.aureus cells become entrapped in autophagosome-like WIPI1 positive vesicles targeted for lysosomal degradation. Plays also a distinct role in controlling the transcription of melanogenic enzymes and melanosome maturation, a process that is distinct from starvation- induced autophagy. May also regulate the trafficking of proteins involved in the mannose-6-phosphate receptor (MPR) recycling pathway. {ECO:0000269|PubMed:15020712, ECO:0000269|PubMed:15602573, ECO:0000269|PubMed:20114074, ECO:0000269|PubMed:20484055, ECO:0000269|PubMed:20639694, ECO:0000269|PubMed:21317285, ECO:0000269|PubMed:22829830, ECO:0000269|PubMed:23088497}.;
Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);XBP1(S) activates chaperone genes;Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

pRec: 0.0945

Intolerance Scores

loftool: 0.612
rvis_EVS: 0.13
rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

pHI: 0.242
hipred: Y
hipred_score: 0.605
ghis: 0.416

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.835

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Wipi1
Phenotype

Gene ontology

Biological process: autophagosome assembly;autophagy of mitochondrion;protein lipidation;autophagy;cellular response to starvation;macroautophagy;protein localization to phagophore assembly site;IRE1-mediated unfolded protein response;vesicle targeting, trans-Golgi to endosome
Cellular component: Golgi membrane;phagophore assembly site;autophagosome membrane;cytoplasm;trans-Golgi network;cytosol;cytoskeleton;endosome membrane;extrinsic component of membrane;clathrin-coated vesicle;phagophore assembly site membrane
Molecular function: signaling receptor binding;protein binding;estrogen receptor binding;phosphatidylinositol-3-phosphate binding;androgen receptor binding;phosphatidylinositol-3,5-bisphosphate binding