WIF1

WNT inhibitory factor 1, the group of Receptor ligands

Basic information

Region (hg38): 12:65050625-65121305

Links

ENSG00000156076 ∙ NCBI:11197 ∙ OMIM:605186 ∙ HGNC:18081 ∙ Uniprot:Q9Y5W5 ∙ 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 WIF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WIF1 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				1	4	5
missense			16	1	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					19	19
Total	0	0	16	2	25

Variants in WIF1

This is a list of pathogenic ClinVar variants found in the WIF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-65051385-C-T			Benign (May 17, 2018)
12-65051390-C-T		not specified	Uncertain significance (Mar 20, 2024)
12-65051392-G-A		not specified	Uncertain significance (May 12, 2024)
12-65051404-G-A		not specified	Uncertain significance (Mar 04, 2024)
12-65051408-G-T			Benign (Jun 18, 2018)
12-65051411-T-C		not specified	Uncertain significance (Sep 14, 2023)
12-65051449-T-C		not specified	Uncertain significance (Jan 20, 2023)
12-65055155-T-C			Likely benign (Jan 19, 2018)
12-65055190-C-T		not specified	Likely benign (May 18, 2022)
12-65055206-G-A			Benign (May 05, 2021)
12-65055291-A-G			Benign (May 16, 2021)
12-65055962-T-C			Benign (May 19, 2021)
12-65056032-C-A		not specified	Uncertain significance (Sep 26, 2023)
12-65056045-T-A		not specified	Uncertain significance (Jun 29, 2023)
12-65056126-C-A		not specified	Uncertain significance (May 14, 2024)
12-65056267-C-CT			Benign (May 19, 2021)
12-65062520-T-C		not specified	Uncertain significance (Aug 22, 2023)
12-65062685-A-G			Benign (May 23, 2021)
12-65066588-A-G			Benign (May 16, 2021)
12-65066685-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-65066899-T-C			Benign (May 19, 2021)
12-65067677-A-G			Benign (May 19, 2021)
12-65067721-C-T		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
12-65067724-T-C		not specified	Uncertain significance (Nov 18, 2022)
12-65067769-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WIF1	protein_coding	protein_coding	ENST00000286574	10	70941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.32e-9	0.569	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.475	185	204	0.906	0.0000104	2466
Missense in Polyphen		81	95.202	0.85082		1191
Synonymous	0.244	70	72.6	0.964	0.00000379	705
Loss of Function	1.22	17	23.4	0.728	0.00000131	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000164	0.000163
South Asian	0.0000328	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to WNT proteins and inhibits their activities. May be involved in mesoderm segmentation.
• Pathway: Wnt signaling pathway - Homo sapiens (human);WNT-Ncore;Wnt-beta-catenin Signaling Pathway in Leukemia;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;wnt signaling pathway;segmentation clock;multi-step regulation of transcription by pitx2;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;Wnt Canonical;Wnt signaling network;TCF dependent signaling in response to WNT;Wnt Mammals;Presenilin action in Notch and Wnt signaling (Consensus)

Recessive Scores

• pRec: 0.222

Intolerance Scores

• loftool: 0.458
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.799
• hipred: N
• hipred_score: 0.493
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wif1
• Phenotype: neoplasm; 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: wif1
• Affected structure: anterior swim bladder bud
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: signal transduction;multicellular organism development;Wnt signaling pathway;negative regulation of Wnt signaling pathway;positive regulation of fat cell differentiation;anatomical structure development
• Cellular component: extracellular region;cell surface
• Molecular function: signaling receptor binding;protein binding;Wnt-protein binding