WNT1

Chr 12

Wnt family member 1

Also known as: BMND16, INT1, OI15

The WNT gene family consists of structurally related genes which 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 very conserved in evolution, and the protein encoded by this gene is known to be 98% identical to the mouse Wnt1 protein at the amino acid level. The studies in mouse indicate that the Wnt1 protein functions in the induction of the mesencephalon and cerebellum. This gene was originally considered as a candidate gene for Joubert syndrome, an autosomal recessive disorder with cerebellar hypoplasia as a leading feature. However, further studies suggested that the gene mutations might not have a significant role in Joubert syndrome. This gene is clustered with another family member, WNT10B, in the chromosome 12q13 region. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtOsteoporosis
UniProtOsteogenesis imperfecta 15

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
2
Active trials
207
Pubs (1 yr)
P/LP submissions
P/LP missense
0.60
LOEUF
LOF
Mechanism· G2P
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GeneReview available — WNT1
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.60LOEUF
pLI 0.326
Z-score 2.55
OE 0.23 (0.100.60)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
1.06Z-score
OE missense 0.79 (0.700.90)
166 obs / 209.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.23 (0.100.60)
00.351.4
Missense OE?0.79 (0.700.90)
00.61.4
Synonymous OE?0.70
01.21.6
LoF obs/exp: 3 / 12.9Missense obs/exp: 166 / 209.1Syn Z: 2.27

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

WNT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.