SETD2 gene spans 147 kb. It is composed of 26 exons encoding three mRNA transcript variants ranging from 8,452 to 8,737 nucleotides in length.

Transcription start is 189 bp for variant 1 and 305 bp for variant 2 upstream of the first ATG of the SETD2 ORF. Variant 2 differs in the 5 UTR and coding sequence compared with variant 1, resulting in a shorter isoform of the SETD2 protein. A third non-coding variant contains an alternate exon compared with variant 1.

No SETD2 pseudogene has been reported.

Human SETD2 is a methyltransferase with 2 main isoforms. Isoform 1 is 2,564 amino acids with a molecular weight of 287.5 kDa. Isoform 2 is 44 residues shorter than isoform 1 at the N-terminus, and is 2520 amino acids with a molecular weight of 282.6 kDa. Three conserved functional domains have been identified in the SETD2: the triplicate AWS-SET-PostSET domains, a WW domain, and a Set2 Rpb1 Interacting (SRI) domain (Li et al., 2016).
The triplicate AWS-SET-PostSET domain mediates methyltransferase activity specific for histone H3 lysine 36 (H3K36) (Edmunds et al., 2008), and a few other non-histone targets (Park et al., 2016). The SET (Suppressor of Variegation, Enhancer of zeste and Trithorax) domain is an evolutionarily conserved motif of 130 amino acids (Rea et al., 2000; Tschiersch et al., 1994), usually present as part of a multi-domain where it is flanked by an AWS (Associated with SET domain) and a PostSET domain. It includes a beta-sheet structure that facilitates multiple rounds of methylation without substrate disassociation (Zhang et al., 2003).
The WW domain, located in the C-terminal region of SETD2, contains two conserved tryptophan (W) residues (Sudol et al., 1995). The WW domain preferentially binds proline-rich segments of other proteins, mediating protein-protein interactions, such as the proline-rich motifs in the Huntingtin protein in Huntingtons disease (Gao et al., 2014).
The SRI domain encompasses a 79 amino acid region towards the C-terminal end of SETD2 and is the primary docking site of RNA Pol II (Li et al., 2005; Kizer et al., 2005). It is composed of a low charged region rich in glutamine and proline. Human SETD2 associates with hyperphosphorylated C-terminal domain (CTD) of RNA polymerase II (RNAPII), linking SETD2 to the transcription elongation process (Li et al., 2002). In yeast, deletion of the CTD region on RNA polymerase II defects trimethylation of H3K36, suggesting that H3K36 trimethylation and transcription elongation are coupled processes (Krogan et al., 2003).

SETD2 is ubiquitously expressed in all human tissues and cell lines tested, including many cancer-derived cell lines. Expression is relatively high in bone marrow, lymph node, testis and thyroid tissue, and it is relatively low in pancreas, heart and salivary gland tissue (Fagerberg et al., 2014).

SETD2 localizes as nuclear speckles and additionally in cytosol.

SETD2 is a lysine methyltransferase and transcriptional regulator involved in histone modification, DNA repair, mRNA regulation, genomic stability, alternative splicing, and interferon-α signaling (Aymard et al., 2014; Skucha, et al., 2019; Luco et al., 2010; de Almeida et al., 2011). The C-terminal end of SETD2 complexes with Heterogeneous Nuclear Ribonucleoprotein L ( HNRNPL) and mediates a non-redundant, co-transcriptional trimethylation to histone H3 at lysine 36 (H3K36me). (Yuan et al., 2009) It was demonstrated that Setd2, the mouse homologue of human Huntingtin-interacting protein HYPB, can modulate all detectable K36me3, but not K36me2 or K36me1, throughout the nucleus using siRNA experiments (Edmunds et al., 2008). Similarly, in yeast, knockdown of Setd2 results in complete absence of H3Kme3 without affecting H3Kme1 or H3Kme2. Loss of SETD2 is associated with greater chromatin accessibility (Carvalho et al., 2014; Simon et al., 2014).
In addition to H3K36, SETD2 methylates two other non-histone targets: the α-tubulin on lysine 40 of mitotic microtubules (Park et al., 2016) and the signal transducer and transcription activator ( STAT1) on lysine 525 (Chen et al., 2017).
SETD2 is also a critical amplifier of interferon-α signaling as STAT1 methylation on lysine 525 catalyzed by SETD2 is an essential signaling event on the induction of interferon stimulating genes, such as ISG15 and MX2 (Chen et al., 2017).
The C-terminal domain of SETD2 has been shown to interact with the tumor suppressor TP53, and modulate the expression of its downstream target genes (Xie et al., 2008; Carvalho et al., 2019).

The AWS-SET-postSET domains in human SETD2 share sequence homology and functional similarity with those in yeast Setd2. The SET domain that mediates methyltransferase activity is a ~130 amino acid sequence motif that is evolutionarily conserved from mammals to yeast and even in some bacteria and viruses (Rea et al., 2000; Tschiersch et al., 1994).

Inactivating SETD2 mutations are common in clear cell renal cell cancer but have been identified also in other cancers including lung cancer, acute lymphoblastic leukemia, and glioma (Fahey and Davis, 2017). The majority of somatic SETD2 mutations are missense mutations (Li et al., 2016). SETD2-deficient cancers exhibit a wide range of mutations, including insertions, deletions, and chromosomal aberrations, suggesting an additional role for SETD2 in genome stability (Li et al., 2016). Homozygous deletion of Setd2 in mice has been shown to result in embryonic lethality (Hu et al., 2010).