WNT8A

Wnt family member 8A, the group of Wnt family

Basic information

Region (hg38): 5:138083989-138092365

Links

ENSG00000061492 ∙ NCBI:7478 ∙ OMIM:606360 ∙ HGNC:12788 ∙ Uniprot:Q9H1J5 ∙ 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 WNT8A gene.

• Inborn genetic diseases (18 variants)
• Hypospadias (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT8A 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in WNT8A

This is a list of pathogenic ClinVar variants found in the WNT8A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-138084096-A-G		not specified	Likely benign (Mar 07, 2023)
5-138084123-G-A		not specified	Uncertain significance (Jun 16, 2023)
5-138084269-A-G		Hypospadias	Uncertain significance (Feb 06, 2022)
5-138084279-C-A		not specified	Uncertain significance (Oct 22, 2021)
5-138084514-C-T		not specified	Uncertain significance (Oct 22, 2021)
5-138084538-A-C		not specified	Uncertain significance (Dec 05, 2022)
5-138084580-G-T		not specified	Uncertain significance (Apr 12, 2022)
5-138087894-A-T		not specified	Uncertain significance (Aug 09, 2021)
5-138089041-A-C		not specified	Uncertain significance (Jul 28, 2021)
5-138090555-T-G		not specified	Uncertain significance (Apr 28, 2022)
5-138090661-C-T		not specified	Uncertain significance (May 30, 2023)
5-138090711-G-A		not specified	Uncertain significance (Aug 17, 2022)
5-138090720-T-C		not specified	Uncertain significance (Jun 11, 2021)
5-138090729-G-A		not specified	Likely benign (Oct 10, 2023)
5-138090735-G-A		not specified	Uncertain significance (Jan 04, 2022)
5-138090762-C-A		not specified	Uncertain significance (Sep 15, 2021)
5-138090835-G-A		not specified	Uncertain significance (Jul 14, 2022)
5-138090849-A-T		not specified	Uncertain significance (Nov 12, 2021)
5-138090892-G-A		not specified	Uncertain significance (Apr 20, 2023)
5-138090926-G-C		not specified	Uncertain significance (Dec 26, 2023)
5-138091015-A-G		not specified	Uncertain significance (May 04, 2023)
5-138091044-G-A		not specified	Uncertain significance (Dec 14, 2023)
5-138091478-G-A		WNT8A-related disorder	Likely benign (May 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT8A	protein_coding	protein_coding	ENST00000398754	6	8474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0102	0.981	125468	0	28	125496	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	159	205	0.778	0.0000111	2331
Missense in Polyphen		63	89.248	0.7059		1031
Synonymous	0.291	73	76.2	0.958	0.00000420	643
Loss of Function	2.29	6	15.8	0.380	7.59e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000270
Ashkenazi Jewish	0.00	0.00
East Asian	0.000279	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000880
Middle Eastern	0.000279	0.000272
South Asian	0.000131	0.000131
Other	0.000330	0.000328

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Plays a role in embryonic patterning. {ECO:0000250|UniProtKB:P51028}.
• 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);WNT-Core;Neural Crest Differentiation;Endoderm Differentiation;EMT transition in Colorectal Cancer;Signaling by GPCR;Signaling by WNT;Signal Transduction;wnt lrp6 signalling;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Disassembly of the destruction complex and recruitment of AXIN to the membrane;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;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.436
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.819
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.542

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wnt8a
• Phenotype: normal phenotype; hearing/vestibular/ear phenotype

Zebrafish Information Network

• Gene name: wnt8a
• Affected structure: neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: regulation of signaling receptor activity;neural crest cell fate commitment;Wnt signaling pathway;neuron differentiation;response to retinoic acid;regulation of transcription involved in anterior/posterior axis specification;canonical Wnt signaling pathway involved in neural crest cell differentiation;cell fate commitment;canonical Wnt signaling pathway;canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment;secondary palate development;beta-catenin destruction complex disassembly
• Cellular component: extracellular region;extracellular space;collagen-containing extracellular matrix
• Molecular function: frizzled binding;receptor ligand activity