WNT7B

Wnt family member 7B, the group of Wnt family

Basic information

Region (hg38): 22:45920366-45977162

Links

ENSG00000188064 ∙ NCBI:7477 ∙ OMIM:601967 ∙ HGNC:12787 ∙ Uniprot:P56706 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WNT7B gene.

• Matthew-Wood syndrome (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT7B 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				4	2	6
missense		1	16			17
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	1	16	4	2

Variants in WNT7B

This is a list of pathogenic ClinVar variants found in the WNT7B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-45922876-C-T		not specified	Uncertain significance (Nov 08, 2021)
22-45922999-C-T		not specified	Uncertain significance (Jan 30, 2024)
22-45923003-C-T			Benign (Dec 31, 2019)
22-45923004-G-A		not specified	Uncertain significance (Mar 02, 2023)
22-45923037-T-C		not specified	Uncertain significance (Feb 07, 2023)
22-45923047-C-T		not specified	Uncertain significance (Jan 17, 2024)
22-45923061-G-A		not specified	Uncertain significance (Jan 04, 2022)
22-45923062-C-T		not specified	Uncertain significance (May 08, 2024)
22-45923133-C-T		not specified	Uncertain significance (Oct 04, 2022)
22-45923156-G-T			Benign (Jun 25, 2018)
22-45923167-G-A		Anophthalmia-microphthalmia syndrome	Likely pathogenic (Aug 31, 2017)
22-45923322-C-T		not specified	Uncertain significance (Mar 11, 2022)
22-45931106-C-T		Matthew-Wood syndrome	Pathogenic (Oct 06, 2021)
22-45931130-T-G		not specified	Uncertain significance (Mar 07, 2024)
22-45931177-C-T		not specified	Uncertain significance (Dec 13, 2021)
22-45931237-G-T		not specified	Uncertain significance (Oct 26, 2021)
22-45931274-C-T		not specified	Uncertain significance (Mar 19, 2024)
22-45931308-G-A			Likely benign (Oct 01, 2023)
22-45931330-G-A		not specified	Uncertain significance (Jun 09, 2022)
22-45949926-G-A		Matthew-Wood syndrome • See cases	Pathogenic (Aug 31, 2017)
22-45949957-G-A			Likely benign (Jul 01, 2022)
22-45949990-C-G		not specified	Uncertain significance (Nov 14, 2023)
22-45949993-G-C		Matthew-Wood syndrome	Pathogenic (Oct 06, 2021)
22-45950055-G-A		not specified	Uncertain significance (Feb 24, 2022)
22-45950131-C-A			Likely benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT7B	protein_coding	protein_coding	ENST00000339464	4	56768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000741	0.983	125701	0	11	125712	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	171	262	0.653	0.0000198	2265
Missense in Polyphen		56	112.56	0.49751		989
Synonymous	-2.02	139	112	1.24	0.00000932	672
Loss of Function	2.12	8	17.6	0.455	0.00000101	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000312	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt/beta- catenin signaling pathway in vascular smooth muscle cells. Required for normal fusion of the chorion and the allantois during placenta development. {ECO:0000250|UniProtKB:P28047}.
• Pathway: Gastric cancer - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Differentiation Pathway;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;EMT transition in Colorectal Cancer;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Signaling by GPCR;Signaling by WNT;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt Canonical;Wnt signaling network;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.601
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.05

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.728
• ghis: 0.673

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.503

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wnt7b
• Phenotype: renal/urinary system phenotype; skeleton phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); respiratory system phenotype; embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: in utero embryonic development;metanephros morphogenesis;activation of JUN kinase activity;regulation of signaling receptor activity;Wnt signaling pathway;establishment or maintenance of polarity of embryonic epithelium;forebrain regionalization;central nervous system vasculogenesis;neuron differentiation;lung development;oxygen homeostasis;regulation of cell projection size;homeostatic process;cellular metabolic process;cell fate commitment;positive regulation of osteoblast differentiation;positive regulation of JNK cascade;fibroblast proliferation;embryonic organ development;neuron projection morphogenesis;synapse organization;response to glucocorticoid;canonical Wnt signaling pathway;lung morphogenesis;lung epithelium development;lobar bronchus development;trachea cartilage morphogenesis;developmental growth involved in morphogenesis;embryonic placenta morphogenesis;chorio-allantoic fusion;mammary gland epithelium development;lens fiber cell development;cellular response to retinoic acid;renal inner medulla development;renal outer medulla development;outer medullary collecting duct development;inner medullary collecting duct development;stem cell proliferation;metanephric collecting duct development;metanephric epithelium development;metanephric loop of Henle development
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi lumen;plasma membrane;endocytic vesicle membrane;extracellular exosome
• Molecular function: frizzled binding;receptor ligand activity