WNT9A

protein-coding

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

Gene summary

The WNT gene family consists of structurally related genes that encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is expressed in gastric cancer cell lines. The protein encoded by this gene shows 75% amino acid identity to chicken Wnt14, which has been shown to play a central role in initiating synovial joint formation in the chick limb. This gene is clustered with another family member, WNT3A, in the chromosome 1q42 region. [provided by RefSeq, Jul 2008]

Previous symbols:

WNT14

MANE transcript

NM_003395.4

Inheritance

—

ClinVar variants

U:69B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr1:227,918,656-227,947,932

External References & Databases

Ensembl (ENSG00000143816)

Transcript & Mutation Effects

hg38 • Region Span ~29.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WNT9A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003395.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense			64 clinvar	1 clinvar		65
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	69	3	1	73

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003395.4	RefSeq	NP_003386.1	4	MANE Select
ENST00000272164.6	Ensembl	ENSP00000272164.5	4	MANE Select
ENST00001143907.1	Ensembl	ENSP00000804096.1	4	Standard
XM_011544271.3	RefSeq	XP_011542573.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
wnt9a	Danio rerio	Structure: chondrocyte Quality: disorganized abnormal

Gene / Model

Organism

Observed Phenotype

wnt9a

Danio rerio

Structure: chondrocyte

Quality: disorganized

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

mitotic cell cycle checkpoint
cell-cell signaling
multicellular organism development
negative regulation of cell population proliferation
regulation of signaling receptor activity

Molecular Function

frizzled binding
receptor ligand activity

Cellular Component

extracellular region
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272164
Coding exons: 4
Length: 29243
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125675
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.20	185	237	0.781	0.0000171	2300
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Intolerance Scores

RVIS EVS: -0.78
RVIS percentile EVS: 12.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.538

Gene Damage Prediction

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