2 or 3 exons spanning 18-21kb genomic DNA.

FAM123B is predicted to generate an mRNA of 8.4kb. The WTX/FAM123B gene is transcribed as a 7.5kb mRNA; an alternatively spliced transcript 831nt shorter has been observed in human primary cell lines, generated by use of a splice donor and splice acceptor site both located within exon 2. Exon 1 is noncoding. The entire ORF of the 7.5kb mRNA is contained within a single exon.

No known pseudogenes.

Two isoforms (858-1135aa) due to alternative splicing. The 858aa WTX isoform 2 lacks amino acids 50-326 of the larger isoform.

Ubiquitous.

Plasma membrane (1135aa isoform), nucleus (858aa isoform).

The N-terminus of the WTX protein has a predicted nuclear localization signal (NLS; residues 166-182), and 2 phosphatidylinositol(4,5)-bisphosphate-binding domains (PtdIns(4,5)P2; residues 2-142 and 143-209) that are involved in its localization to the plasma membrane. The WTX protein also has 3 adenomatous polyposis coli (APC) binding domains (APCBD1, residues 280-368; APCBD2, 380-531; and APCBD3, 717-834) that mediate its interaction with the armadillo (ARM) repeats of the tumor suppressor APC, as well as a beta-catenin binding site (located between residue 367 and the C-terminus), an acidic domain (residues 370-411), two coiled-coil domains (residues 374-403 and 574-593) and a proline-rich region (residues 951-1104).
The 858aa isoform is missing both PtdIns(4,5)P2 binding domains and localizes to the nucleus in a punctate pattern. Interestingly, this shorter isoform lacks the predicted NLS, and the longer isoform that includes the predicted NLS localizes to the plasma membrane.
WTX forms a protein complex with beta-catenin, AXIN1, beta-transducin repeat-containing protein 2 (beta-TrCP2) and APC and negatively regulates the WNT signaling pathway by promoting the ubiquitination and degradation of beta-catenin. WTX also plays a role in the recruitment of APC from microtubules to the plasma membrane and appears to be involved in the maintenance of intercellular junctions.

The amino terminus of WTX shows homology to FAM123A; 32% identical over 586aa. The regions with the highest percentage identity include the predicted NLS, the APCBD1 and APCBD2 binding domains, and the acidic domain.

Mutational analysis of the WTX gene in gastric, colorectal, and hepatocellular carcinomas and in acute myelogenous leukemia (AML) and acute lymphoblastic leukemia (ALL) showed no deletion or truncating mutations of WTX. Missense mutations were found in 1/47 colorectal carcinomas and 1/60 normal karyotype AML cases. Various missense mutations (D233Y, K292N, E395D, R584G, Y599C, P880L, P884L, and I1003M) found in Wilms tumors were also in most cases found in normal tissues from the same patient. The missense mutations seen in the one colorectal carcinoma and one AML were tumor-specific. Although these are not currently known to be SNPs (dbSNP, build 129), they may not constitute functional mutations in WTX.
Inactivating mutations in WTX (deletions and truncating/frameshift mutations) appear to be negatively correlated in Wilms tumors with activating mutations in exon 3 of CTNNB1 (encoding beta-catenin), implicating the activation of the WNT signaling pathway in the formation of Wilms tumors since both inactivating mutations of WTX and activating mutations of CTNNB1 function to activate this signaling pathway.

In osteopathia striata congenita with cranial stenosis (OSCS), deletions of the entire WTX gene and truncation mutations (nonsense mutations and deletion/insertion + frameshift mutations) have been observed. In cases with truncation mutations in which the mutations affect nucleotides 285-1112 (encoding residues 50-326), the mutations reside within intron 2 of the shorter alternatively spliced transcript and do not affect the 858aa isoform. However, such mutations are lethal in males and demonstrate a typical clinical phenotype in females, suggesting that retention of the wild-type 858aa isoform of WTX cannot compensate in terms of regulation of the WNT signaling pathway for loss or truncation of the 1135aa isoform.

In Wilms tumors, the most commonly observed mutation is the deletion of the entire WTX gene. Truncation mutations and missense mutations have also been observed.