WIPI2

WD repeat domain, phosphoinositide interacting 2, the group of WD repeat domain containing|WIPI family|Autophagy related

Basic information

Region (hg38): 7:5190196-5233840

Links

ENSG00000157954

∙ NCBI:26100 ∙ OMIM:609225 ∙ HGNC:32225 ∙ Uniprot:Q9Y4P8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual developmental disorder with short stature and variable skeletal anomalies (Limited), mode of inheritance: AR
intellectual developmental disorder with short stature and variable skeletal anomalies (Limited), mode of inheritance: AR
intellectual developmental disorder with short stature and variable skeletal anomalies (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with short stature and variable skeletal anomalies	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Musculoskeletal	30968111

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WIPI2 gene.

not_specified (47 variants)
not_provided (14 variants)
WIPI2-related_disorder (12 variants)
Intellectual_developmental_disorder_with_short_stature_and_variable_skeletal_anomalies (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WIPI2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015610.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	5 clinvar	13
missense	2 clinvar		47 clinvar	2 clinvar	2 clinvar	53
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	0	48	10	7

Highest pathogenic variant AF is 0.000004965243

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WIPI2	protein_coding	protein_coding	ENST00000288828	13	43639

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00639	0.993	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	204	283	0.722	0.0000178	2951
Missense in Polyphen		19	48.848	0.38896		540
Synonymous	-0.986	140	126	1.11	0.00000958	893
Loss of Function	2.94	8	23.3	0.343	0.00000109	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.000110	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Early component of the autophagy machinery being involved in formation of preautophagosomal structures and their maturation into mature phagosomes in response to phosphatidylinositol 3-phosphate (PtdIns3P). May bind PtdIns3P. {ECO:0000269|PubMed:20505359}.;
Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

pRec: 0.0854

Intolerance Scores

loftool: 0.636
rvis_EVS: -1.07
rvis_percentile_EVS: 7.43

Haploinsufficiency Scores

pHI: 0.100
hipred: Y
hipred_score: 0.639
ghis: 0.558

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.928

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Wipi2
Phenotype

Gene ontology

Biological process: autophagosome assembly;autophagy of mitochondrion;protein lipidation;cellular response to starvation;macroautophagy;protein localization to phagophore assembly site;protein lipidation involved in autophagosome assembly;autophagosome maturation;xenophagy
Cellular component: phagophore assembly site;nucleoplasm;autophagosome;cytosol;membrane;extrinsic component of membrane;protein-containing complex;phagophore assembly site membrane
Molecular function: protein binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,5-bisphosphate binding