WTIP

WT1 interacting protein, the group of Ajuba family

Basic information

Region (hg38): 19:34481758-34512304

Links

ENSG00000142279 ∙ NCBI:126374 ∙ OMIM:614790 ∙ HGNC:20964 ∙ Uniprot:A6NIX2 ∙ 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 WTIP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WTIP 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in WTIP

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

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

Position	Type	Phenotype	Significance	ClinVar
19-34482014-C-G		not specified	Uncertain significance (Jul 13, 2021)
19-34482045-A-G		not specified	Uncertain significance (Dec 28, 2023)
19-34482047-C-G		not specified	Uncertain significance (Mar 16, 2022)
19-34482159-G-A		not specified	Uncertain significance (Dec 02, 2021)
19-34482161-G-A		not specified	Uncertain significance (May 16, 2022)
19-34482192-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-34482210-C-T		not specified	Uncertain significance (Oct 14, 2023)
19-34482234-G-A		not specified	Uncertain significance (Apr 28, 2023)
19-34482287-G-A		not specified	Uncertain significance (May 11, 2022)
19-34482333-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-34482451-C-G		not specified	Likely benign (Sep 17, 2021)
19-34482509-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-34482516-C-T		not specified	Uncertain significance (Apr 04, 2024)
19-34482522-C-T		not specified	Uncertain significance (Oct 30, 2023)
19-34482549-A-G		not specified	Uncertain significance (May 30, 2023)
19-34482593-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-34490408-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-34490438-A-T		not specified	Uncertain significance (Oct 05, 2023)
19-34490468-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-34493091-A-C		not specified	Uncertain significance (Jun 11, 2024)
19-34493266-T-G		not specified	Uncertain significance (Feb 14, 2023)
19-34493550-A-G		not specified	Uncertain significance (Sep 06, 2022)
19-34493579-G-A		not specified	Uncertain significance (Jun 28, 2023)
19-34493585-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-34494587-G-A		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WTIP	protein_coding	protein_coding	ENST00000590071	8	25385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000667	0.914	125439	0	25	125464	0.0000996

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.606	128	149	0.860	0.00000982	2629
Missense in Polyphen		81	96.915	0.83578		1039
Synonymous	-0.338	64	60.7	1.06	0.00000454	945
Loss of Function	1.58	9	15.8	0.571	9.55e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000380	0.000364
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000110
Finnish	0.0000812	0.0000463
European (Non-Finnish)	0.0000800	0.0000792
Middle Eastern	0.000111	0.000110
South Asian	0.000131	0.000131
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing. Negatively regulates Hippo signaling pathway and antagonizes phosphorylation of YAP1. Acts as a transcriptional corepressor for SNAI1 and SNAI2/SLUG-dependent repression of E-cadherin transcription. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. In podocytes, may play a role in the regulation of actin dynamics and/or foot process cytoarchitecture (By similarity). In the course of podocyte injury, shuttles into the nucleus and acts as a transcription regulator that represses WT1-dependent transcription regulation, thereby translating changes in slit diaphragm structure into altered gene expression and a less differentiated phenotype. Involved in the organization of the basal body (By similarity). Involved in cilia growth and positioning (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:A9LS46, ECO:0000269|PubMed:20303269, ECO:0000269|PubMed:20616046, ECO:0000269|PubMed:21834987, ECO:0000269|PubMed:22286099}.
• Pathway: Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human);Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Cellular response to hypoxia;Cellular responses to stress;Cellular responses to external stimuli (Consensus)

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.319
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.822

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wtip
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: wtip
• Affected structure: ciliated cell
• Phenotype tag: abnormal
• Phenotype quality: increased angle to

Gene ontology

• Biological process: response to hypoxia;cytoskeleton organization;regulation of cell morphogenesis;cell projection organization;gene silencing by miRNA;negative regulation of hippo signaling;negative regulation of nucleic acid-templated transcription;positive regulation of gene silencing by miRNA
• Cellular component: P-body;nucleus;transcription factor complex;cell-cell junction;adherens junction
• Molecular function: transcription corepressor activity;protein binding;metal ion binding