The genes for MSH2 and MSH6 which form the major mismatch recognition MutSalpha complex functional in the mismatch repair (MMR) pathway are located within 1 Mb of each other. MSH2 and MSH6 may have been produced by duplication of a primordial mutS repair gene.

MSH6 gene maps to NC_000002.10 and spans a region of 23.8 kilo bases.
MSH6 has 10 exons, the sizes being 347, 197, 170, 2545, 266, 119, 89, 155, 200 and 176 bps.

Human MSH6 gene is transcriptionally upregulated 2.5 fold at late G1/early S phase while the amount of protein remains unchanged during the whole cell cycle.
The promoter region has a high GC content, as well as multiple start sites. Sequence analysis of 3.9 kb of the 5-upstream region of the MSH6 gene revealed the absence of TATAA- or CAAT-boxes. Seven consensus binding sequences for the ubiquitous transcription factor Sp1 were found in the promoter region. This factor is implicated in positioning the RNA polymerase II complex at the transcriptional start sites of promoters lacking TATA- and CAAT-boxes. The proximal promoter region of MSH6 gene also contains several consensus binding sites of the embryonic TEA domain-containing factor ETF. This transcription factor has also been reported to stimulate transcription from promoters lacking the TATA box. In addition, the trancription of MSH6 gene is downregulated by CpG methylation of the promoter region.
Three common polymorphic variants (-557 T G, -448 G A, and -159 C T) of the MSH6 promoter have been identified in which different Sp1 sites were inactivated by single-nucleotide polymorphisms (SNPs) resulting in altered promoter activity.

No pseudogene has been reported for the MSH6 gene.

Eukaryotic MutSalpha is a heterodimer of the 100-kDa MSH2 and the 160-kDa MSH6 that participates in the mismatch repair pathway. The proteins are required for single base and frameshift mispair specific binding, a result consistent with the finding that tumour-derived cell lines devoid of either protein have a mutator phenotype.

The MSH6 protein maps to NP_000170 and has 1360 amino acids. The molecular weight is 152786 Da. The protein contains a highly conserved helix-turn-helix domain associated with a Walker-A motif (an adenine nucleotide and magnesium binding motif) with ATPase activity.
The breast cancer 1 gene (BRCA1) product is part of a large multisubunit protein complex of tumor suppressors, DNA damage sensors, and signal transducers. This complex is called BASC, for BRCA1-associated genome surveillance complex and the mismatch repair protein MSH6 was found to be a part of this complex.

The subcellular localisation of MSH6 is the nucleus.

hMSH6 gene product with hMSH2, hMSH3 gene products play role in strand specific repair of DNA replication errors. Studies show that hMSH2-hMSH6 complex functions in the recognition step of the repair of base-base mismatches or single frameshifts. The ADP/ATP binding domain of the heterodimer and the associated ATPase activity function to regulate mismatch binding as a molecular switch. Both MSH2 and MSH6 can simultaneously bind ATP. The MSH6 subunit contains the high-affinity ATP binding site and MSH2 contains a high-affinity ADP binding site. Stable binding of ATP to MSH6 results in a decreased affinity of MSH2 for ADP, and binding to mispaired DNA stabilizes the binding of ATP to MSH6. Mispair binding encourages a dual-occupancy state with ATP bound to Msh6 and Msh2; following which there is a hydrolysis-independent sliding along DNA. Subsequent steps result in the excision of the mispaired region followed by DNA synthesis and ligation.

H.sapiens: MSH6 (mutS homolog 6 (E. coli)).
C.familiaris: LOC474585 (similar to mutS homolog 6).
M.musculus: Msh6 (mutS homolog 6 (E. coli)).
C.elegans: msh-6 (MSH (MutS Homolog) family).
S.pombe: SPCC285.16c (hypothetical protein).
S.cerevisiae: MSH6 (Mismatch repair protein).
A.thaliana: MSH6 (MSH6).

The MSH6 gene plays a role in the development of inherited cancers, especially the colorectum and endometrial cancers.

MSH6 germline mutations have variable penetration. Atypical hereditary non polyposis colorectal cancer (HNPCC) can result from germline mutations in MSH6; however, disease-causing germline mutations of MSH6 are rare in HNPCC and HNPCC-like families. Other studies have indicated that germline MSH6 mutations may contribute to a subset of early-onset colorectal cancer.

The involvement of somatic or epigenetic inactivation of hMSH6 is rare in colorectal cancer and missense mutations in MSH6 are often clinically innocuous or have a low penetrance. However, somatic mutations of MSH6 have been shown to confer resistance to alkylating agents such as temozolomide in malignant gliomas in vivo. This concurrently results in accelerated mutagenesis in resistant clones as a consequence of continued exposure to alkylating agents in the presence of defective mismatch repair. Therefore, when MSH6 is inactivated in gliomas, there is a change in status of the alkylating agents from induction of tumour cell death to promotion of neoplastic progression.