TM6SF2

TM6SF2
Identifiers
Aliases	TM6SF2, transmembrane 6 superfamily member 2
External IDs	OMIM: 606563 MGI: 1933210 HomoloGene: 77694 GeneCards: TM6SF2
Gene location (Human)
Chr.	Chromosome 19 (human)[1]
End	19,273,391 bp[1]
Gene location (Mouse)
Chr.	Chromosome 8 (mouse)[2]
End	70,080,066 bp[2]
Gene ontology
Molecular function	• molecular function; • GO:0001948 protein binding;
Cellular component	• integral component of membrane; • endoplasmic reticulum-Golgi intermediate compartment membrane; • endoplasmic reticulum membrane; • endoplasmic reticulum; • membrane;
Biological process	• regulation of lipid metabolic process; • lipid metabolism; • lipid homeostasis;
	Sources:Amigo / QuickGO
Orthologs
	53345
	107770
	ENSG00000213996
	ENSMUSG00000036151
	Q9BZW4
	Q8R1J1
	NM_203510; NM_001001524
	NM_001293795; NM_181540
	NP_001001524
	NP_001280724; NP_853518
	Wikidata
View/Edit Human	View/Edit Mouse

TM6SF2 is the Transmembrane 6 superfamily 2 human gene which codes for a protein by the same name. This gene is otherwise called KIAA1926.[5] Its exact function is currently unknown.

Location

TM6SF2 is located on chromosome 19 precisely at locus 19p13.3-p12. It is flanked by SUGP1 (a SURP and G-Patch Domain-Containing protein thought to play a role in pre-mRNA splicing [5]) and HAPLN4 (a hyaluronan and proteoglycan link protein 4 that binds to hyaluronic acid and may be involved in formation of the extracellular matrix [5]) genes upstream and downstream respectively.[6]

Evolutionary aspects

Orthologs

TM6SF2 is a moderately conserved gene. There exist orthologs in several phyla as far diverged as invertebrates. 82 organisms have been identified as having orthologs of this gene. The most distant orthologs of TM6SF2 are in zebra fish (Danio rerio) and the deer tick (Ixodes scapularis).[6] Below is a summary table of some of the gene orthologs obtained from the NCBI database.

Scientific Name	Common Name	Divergence date (MYA)	NCBI [6] accession number	Sequence Length	Percent Identity	Percent Similarity
Homo sapiens	Human	0	NP_001001524.2	377	100	100
Pan troglodytes	Chimpanzee	6.3	XP_001140342.2	377	99	99
Mus musculus	Mouse	92.3	XP_003125904	378	79	87
Ceratotherium simum simum	Southern white rhinoceros	94.2	XP_004422975.1	376	89	92
Capra hircus	Goat	94.2	XP_005682141.1	343	89	86
Myotis davidii	Mouse-eared bat	94.2	XP_006778388.1	338	86	91
Mustela putorius furo	Domestic ferret	94.2	XP_004760922.1	376	84	89
Vicugna pacos	Alpaca	94.2	XP_006199087.1	376	84	89
Canis lupus familiaris	Dog	94.2	XP_852125.1	376	83	89
Orcinus orca	Killer whale	94.2	XP_004277546.1	376	82	88
Bos taurus	Cow	94.2	XP_005208509.1	376	74	80
Loxodonta africana	African savanna elephant	98.7	XP_003413566.1	377	90	93
Alligator mississipiens	American alligator	296	XP_006271093.1	346	67	79
Ophiophagus hannah	King cobra	296	ETE70999	292	25.3	?
Gallus gallus	Chicken	296	XP_423447.3	374	62	74
Falco peregrinus	Peregrine falcon	296	XP_005244205.1	376	59	73
Xenopus tropicalis	Western-clawed frog	371.2	XP_004760922.1	375	58	74
Danio rerio	Zebrafish	400.1	NP_001074130	374	44.3	?
Latimeria chalumnae	Coelocanth	414.9	XP_005989673.1	327	63	75
Ixodes scapularis	Deer tick	782.7	XP_002406440.1	113	45.1	?

Paralogs

TM6SF1 has been identified as a paralog of TM6SF2 in humans [6] about which little is known.

Homologous domains

The domain of unknown function DUF2781 is highly conserved across homologs. DUF2781 belongs to the pfam10914 family which comprises uncharacterized eukaryotic proteins, some of which are membrane proteins [6]

mRNA

The RNA product is 1483 base pairs long and is spliced alternatively to yield seven different isoforms (alternative mRNAs a - f with form a being the most abundant) with varying combinations of the 10 identified exons.[7] The microRNA miR-1343 binds to a 3’ UTR site called 7mer-m8 (as predicted by TargetScan[8]).

Folding patterns

The 5' and 3' UTR regions of the mRNA show some stem loop formation for stability. Much of this chemistry appears to be taking place in the 5' region which has three stem loops compared to the 3' region with only one.[9]

Exons and introns

There are ten different exons and the ones expressed depend on how alternative splicing proceeds. There are four alternative polyadenylation sites present.[7]

Promoter region

The promoter for this gene is upstream and spans bases 19383923 to 19384700 (778 bp long) on the minus strand of chromosome 19. There exist several transcription factors capable of binding to this promoter region including cAMP responsive element binding protein, SMAD3, KLF3, EGR1, SOX/SRY, PAX2/PAX5[10] and two SNP regions have been identified as well.[11] The transcription factors predicted to bind the TM6SF2 promoter suggest this protein functions in growth and tumor regulation as well as sex determination to a lesser extent.

Protein

The TM6SF2 protein contains 377 amino acids and is 42,554 Da large with an isoelectric point of about 7.7.[12]

Domains and motifs

There is a domain of unknown function, DUF2781 ( pfam10914 family) spanning amino acids 218 to 359 in the C-terminus of the protein.[6] There are nine transmembrane regions in this protein. The first one contains the signal peptide which is eventually cleaved following protein localization to the ER. A terminal KHHQ sequence is an endoplasmic reticulum retention signal.[13]

Conceptual TM6SF2 protein with phosphorylation sites

Secondary structure

Several alpha helices and beta strands are formed by the mature protein with as many as thirteen helices (including transmembrane helices) and fifteen beta sheets predicted.[14]

3° and 4° structure

The protein side groups in this protein do not necessarily interact in a manner to form tertiary and quaternary structures. The cysteines present are not predicted to form stable disulfide bonds.[15]

Post-translational modifications

Two main post-translational modifications occur; phosphorylation at tyrosine, serine and tryptophan sites and two low probability sumoylation sites.[16]

Expression patterns

In humans, TM6SF2 expression has been documented in the adult stage only specifically in the intestine and liver in moderate amounts as well as embryonic tissue and ovary at low levels. Other sources indicate expression in brain, lung, testis, stomach, heart, colon, kidney and adipose tissue.[17]

Protein subcellular localization studies with confocal microscopy demonstrated that TM6SF2 is localized in the endoplasmic reticulum and the ER-Golgi intermediate compartment of human liver cells.[18]

Protein interactions

No known protein-protein interactions have been established thus far.[19][20][21]

Clinical significance

In a study that used pre-made kits to predict cardiac allograft rejection using peripheral blood only, graft rejection was associated with decreased levels of TM6SF2 expression, alongside other genes.[22]

A variant TM6SF2 gene causes susceptibility to nonalcoholic fatty liver disease due to impaired very low density lipoprotein (VLDL) production14.[23]

TM6SF2 inhibition was associated with reduced secretion of TG-rich lipoproteins (TRLs) and increased cellular TG concentration and lipid droplet content, whereas TM6SF2 overexpression reduced liver cell steatosis. TM6SF2 is a regulator of liver fat metabolism with opposing effects on the secretion of TRLs and hepatic lipid droplet content.[18]

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References

GRCh38: Ensembl release 89: ENSG00000213996 - Ensembl, May 2017
GRCm38: Ensembl release 89: ENSMUSG00000036151 - Ensembl, May 2017
"Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
"Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
GeneCards® The Human Database Compendium website https://www.genecards.org/
National Center for Biotechnology Information, U.S. National Library of Medicine website https://www.ncbi.nlm.nih.gov/
National Center for Biotechnology Information, U.S. National Library of Medicine website. AceView program.https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
Agarwal V, Bell GW, Nam JW, Bartel DP (August 2015). "Predicting effective microRNA target sites in mammalian mRNAs". eLife. 4: e05005. doi:10.7554/eLife.05005. PMC 4532895. PMID 26267216.
mfold web server: 1995-2014 , Michael Zuker & Nick Markham, © Rensselaer Polytechnic Institute. Hosted by The RNA Institute, College of Arts and Sciences, State University of New York at Albany.http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form
Genomatix Gene2Promoter program. http://www.genomatix.de/
National Center for Biotechnology Information, U.S. National Library of Medicine website. SNP:GeneView program.https://www.ncbi.nlm.nih.gov/SNP/
San Diego Super Computer (SDSC) Biology Workbench online program. SAPS protein assessment program.http://workbench.sdsc.edu/
Petersen TN, Brunak S, von Heijne G, Nielsen H (September 2011). "SignalP 4.0: discriminating signal peptides from transmembrane regions". Nature Methods. 8 (10): 785–6. doi:10.1038/nmeth.1701. PMID 21959131.
San Diego Super Computer (SDSC) Biology Workbench online program. CHOFAS program.
DISULFIND program: Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a Disulfide Bonding State and Cysteine Connectivity Prediction Server, Nucleic Acids Research, 34(Web Server issue):W177--W181, 2006.http://disulfind.dsi.unifi.it/
ExPASy Bioinformatics Resource Portal. Proteomics tool. http://expasy.org/proteomics
National Center for Biotechnology Information, U.S. National Library of Medicine website. GEO Profiles.https://www.ncbi.nlm.nih.gov/geoprofiles
Mahdessian H, Taxiarchis A, Popov S, Silveira A, Franco-Cereceda A, Hamsten A, Eriksson P, van't Hooft F (June 2014). "TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content". Proceedings of the National Academy of Sciences of the United States of America. 111 (24): 8913–8. doi:10.1073/pnas.1323785111. PMC 4066487. PMID 24927523.
MINT program "Archived copy". Archived from the original on 2006-05-06. Retrieved 2011-05-09.CS1 maint: archived copy as title (link)
IntAct program http://www.ebi.ac.uk/intact/
STRING program http://string.embl.de/
US patent office. Predictors of transplant rejection determined by peripheral blood gene-expression profiling. Publication number; US8053182 B2. Publication type; Grant. Application number; US 10/587,569. PCT number; PCT/US2005/002697. Publication date; Nov 8, 2011. Inventors; Thomas Cappola, Jonathan A. Epstein.
Kozlitina J, Smagris E, Stender S, Nordestgaard BG, Zhou HH, Tybjærg-Hansen A, Vogt TF, Hobbs HH, Cohen JC (April 2014). "Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease". Nature Genetics. 46 (4): 352–6. doi:10.1038/ng.2901. PMC 3969786. PMID 24531328.

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[refGRCh38Ensembl-1] GRCh38: Ensembl release 89: ENSG00000213996 - Ensembl, May 2017

[refGRCm38Ensembl-2] GRCm38: Ensembl release 89: ENSMUSG00000036151 - Ensembl, May 2017

[3] "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[4] "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[Genecards-5] GeneCards® The Human Database Compendium website https://www.genecards.org/

[NCBI-6] National Center for Biotechnology Information, U.S. National Library of Medicine website https://www.ncbi.nlm.nih.gov/

[AceView-7] National Center for Biotechnology Information, U.S. National Library of Medicine website. AceView program.https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/

[8] Agarwal V, Bell GW, Nam JW, Bartel DP (August 2015). "Predicting effective microRNA target sites in mammalian mRNAs". eLife. 4: e05005. doi:10.7554/eLife.05005. PMC 4532895. PMID 26267216.

[9] web server: 1995-2014 , Michael Zuker & Nick Markham, © Rensselaer Polytechnic Institute. Hosted by The RNA Institute, College of Arts and Sciences, State University of New York at Albany.http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form

[10] Genomatix Gene2Promoter program. http://www.genomatix.de/

[11] National Center for Biotechnology Information, U.S. National Library of Medicine website. SNP:GeneView program.https://www.ncbi.nlm.nih.gov/SNP/

[12] San Diego Super Computer (SDSC) Biology Workbench online program. SAPS protein assessment program.http://workbench.sdsc.edu/

[13] Petersen TN, Brunak S, von Heijne G, Nielsen H (September 2011). "SignalP 4.0: discriminating signal peptides from transmembrane regions". Nature Methods. 8 (10): 785–6. doi:10.1038/nmeth.1701. PMID 21959131.

[14] San Diego Super Computer (SDSC) Biology Workbench online program. CHOFAS program.

[15] DISULFIND program: Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a Disulfide Bonding State and Cysteine Connectivity Prediction Server, Nucleic Acids Research, 34(Web Server issue):W177--W181, 2006.http://disulfind.dsi.unifi.it/

[16] ExPASy Bioinformatics Resource Portal. Proteomics tool. http://expasy.org/proteomics

[17] National Center for Biotechnology Information, U.S. National Library of Medicine website. GEO Profiles.https://www.ncbi.nlm.nih.gov/geoprofiles

[Mahdessian_2014-18] Mahdessian H, Taxiarchis A, Popov S, Silveira A, Franco-Cereceda A, Hamsten A, Eriksson P, van't Hooft F (June 2014). "TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content". Proceedings of the National Academy of Sciences of the United States of America. 111 (24): 8913–8. doi:10.1073/pnas.1323785111. PMC 4066487. PMID 24927523.

[19] MINT program "Archived copy". Archived from the original on 2006-05-06. Retrieved 2011-05-09.CS1 maint: archived copy as title (link)

[20] IntAct program http://www.ebi.ac.uk/intact/

[21] STRING program http://string.embl.de/

[22] US patent office. Predictors of transplant rejection determined by peripheral blood gene-expression profiling. Publication number; US8053182 B2. Publication type; Grant. Application number; US 10/587,569. PCT number; PCT/US2005/002697. Publication date; Nov 8, 2011. Inventors; Thomas Cappola, Jonathan A. Epstein.

[23] Kozlitina J, Smagris E, Stender S, Nordestgaard BG, Zhou HH, Tybjærg-Hansen A, Vogt TF, Hobbs HH, Cohen JC (April 2014). "Exome-wide association study identifies a TM6SF2 variant that confers susceptibility to nonalcoholic fatty liver disease". Nature Genetics. 46 (4): 352–6. doi:10.1038/ng.2901. PMC 3969786. PMID 24531328.