WNT9A

Wnt family member 9A, the group of Wnt family|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:227918656-227947932

Previous symbols: [ "WNT14" ]

Links

ENSG00000143816

∙ NCBI:7483 ∙ OMIM:602863 ∙ HGNC:12778 ∙ Uniprot:O14904 ∙ 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 WNT9A gene.

not_specified (55 variants)
not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT9A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003395.4. 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				2 clinvar	1 clinvar	3
missense			54 clinvar	1 clinvar		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	54	3	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WNT9A	protein_coding	protein_coding	ENST00000272164	4	29243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.912	0.0876	125673	0	2	125675	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	185	237	0.781	0.0000171	2300
Missense in Polyphen		77	109.77	0.70149		1024
Synonymous	0.00502	99	99.1	0.999	0.00000703	754
Loss of Function	2.97	1	12.2	0.0818	6.72e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Required for normal timing of IHH expression during embryonic bone development, normal chondrocyte maturation and for normal bone mineralization during embryonic bone development. Plays a redundant role in maintaining joint integrity. {ECO:0000250|UniProtKB:O42280, ECO:0000250|UniProtKB:Q8R5M2}.;
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);EMT transition in Colorectal Cancer;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;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt Canonical;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Intolerance Scores

loftool
rvis_EVS: -0.78
rvis_percentile_EVS: 12.88

Haploinsufficiency Scores

pHI: 0.0893
hipred: Y
hipred_score: 0.699
ghis: 0.561

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.538

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Wnt9a
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); skeleton phenotype; craniofacial phenotype;

Zebrafish Information Network

Gene name: wnt9a
Affected structure: chondrocyte
Phenotype tag: abnormal
Phenotype quality: disorganized

Gene ontology

Biological process: mitotic cell cycle checkpoint;cell-cell signaling;multicellular organism development;negative regulation of cell population proliferation;regulation of signaling receptor activity;Wnt signaling pathway;neuron differentiation;negative regulation of chondrocyte differentiation;embryonic forelimb morphogenesis;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;cell fate commitment;positive regulation of cell differentiation;positive regulation of smoothened signaling pathway;embryonic skeletal system morphogenesis;canonical Wnt signaling pathway;iris morphogenesis;cornea development in camera-type eye;cellular response to retinoic acid;embryonic skeletal joint development
Cellular component: extracellular region;extracellular space
Molecular function: frizzled binding;receptor ligand activity