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.

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.

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				2	1	3
missense			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	3	1

Variants in WNT9A

This is a list of pathogenic ClinVar variants found in the WNT9A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-227921526-T-C		not specified	Uncertain significance (Jun 29, 2022)
1-227921532-T-C		not specified	Uncertain significance (May 13, 2024)
1-227921620-G-T		not specified	Uncertain significance (Oct 11, 2021)
1-227921627-G-A		not specified	Uncertain significance (May 17, 2023)
1-227921672-C-T		not specified	Uncertain significance (Apr 17, 2024)
1-227921680-C-A		not specified	Uncertain significance (May 24, 2024)
1-227921715-C-A		not specified	Uncertain significance (Oct 05, 2021)
1-227921762-C-T		not specified	Uncertain significance (Apr 20, 2024)
1-227921771-G-A		not specified	Uncertain significance (Oct 26, 2022)
1-227921870-G-A		not specified	Uncertain significance (Apr 18, 2024)
1-227921915-G-A		not specified	Uncertain significance (May 27, 2022)
1-227921934-T-A		not specified	Uncertain significance (May 24, 2024)
1-227921987-C-A		not specified	Uncertain significance (Jan 24, 2024)
1-227924188-T-C		not specified	Uncertain significance (Nov 10, 2022)
1-227924197-G-A		not specified	Uncertain significance (Jun 16, 2024)
1-227924222-C-T			Likely benign (Dec 01, 2022)
1-227924319-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-227924333-C-T			Benign (Jul 13, 2018)
1-227925372-C-T			Likely benign (Mar 01, 2023)
1-227925373-G-A		not specified	Uncertain significance (Jul 17, 2023)
1-227925388-G-A		not specified	Uncertain significance (Apr 06, 2022)
1-227925398-G-A		not specified	Uncertain significance (Oct 10, 2023)
1-227925403-A-C		not specified	Uncertain significance (Feb 10, 2022)
1-227925409-C-T		not specified	Uncertain significance (Jan 11, 2023)
1-227925433-C-T		not specified	Uncertain significance (Oct 22, 2021)

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

• 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