Table 1 Protein-coding genes and functions on the human Y chromosome
Gene ID | Gene symbol | Gene name | Chr location (order:Yp - Yq) | Mouse ortholog (Chromosome) | Gene descriptiona |
|---|---|---|---|---|---|
55344 | PLCXD1 | Phosphatidylinositol specific phospholipase C X domain containing 1 | Yp11.32-p11.31 | Plcxd1 (chr 5) | A protein-coding gene at the most terminus of PAR1, encoding an enzyme catalyzes the formation of 1,4,5-trisphosphate and diacylglycerol from phosphatidyinositol 4,5-bisphosphate, involved in intracellular transduction of extracellular signals |
8225 | GTPBP6 | GTP binding protein 6 (putative) | Yp11.31 | Gtpbp6 (chr 5) | A PAR1 gene coding for a GTP binding protein, potentially associated with verbal ability and cognition |
28227 | PPP2R3B | Protein phosphatase 2 regulatory subunit B” beta | Yp11.31 | Ppp2rla (chr 17) | A PAR1 gene encoding the protein phosphatase 2, one of the four major Ser/Thr phosphatases, likely inovlved in the negative control of cell growth and division |
6473 | SHOX | Short stature homeobox | Yp11.2 | Shox2 (chr 3) | A PAR1 gene encoding a protein of the paired homeobox family, defects in this gene are associated with idiopathic growth retardation and in the short stature phenotype of Turner syndrome patients |
64109 | CRLF2 | Cytokine receptor like factor 2 | Yp11.2 | Crlf2 (chr 5) | A PAR1 gene encoding a member of the type I cytokine receptor family and a receptor for thymic stromal lymphopoietin (TSLP), associated with acute lymphoblastic leukemia and Down syndrome |
1438 | CSF2RA | Colony stimulating factor 2 receptor subunit alpha | Yp11.2 | Csf2ra (chr 19) | A PAR1 gene encoding for the alpha subunit of the heterodimeric receptor for colony stimulating factor 2 (CSF2), a cytokine controlling the production, differentiation, and function of granulocytes and macrophages; and associated with Surfactant metabolism dysfunction type 4 |
3563 | IL3RA | Interleukin 3 receptor subunit alpha | Yp11.2 | Il3ra (chr 14) | A PAR1 gene encoding an interleukin 3 specific subunit of a heterodimeric cytokine receptor; and a leukemia-associated antigen (CD123) highly expressed in leukemic stem cells and blasts |
293 | SLC25A6 | Solute carrier family 25 member 6 | Yp11.2 | Slc25a5 (chr X) | A PAR1 gene encoding a member of the mitochondrial carrier subfamily of solute carrier proteins, functions as a gated pore for translocation of ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm, likely involved in the permability transition pore complex and apoptosis |
8623 | ASMTL | Acetylserotonin O-methyltransferase like | Yp11.2 | A PAR1 gene encoding a protein with an N-terminus similar to the multicopy associated filamentation (maf) protein of Bacillus subtilis and to orfE of E. coli and a C-terminus similar to N-acetylserotonin O-methyltransferase | |
286530 | P2RY8 | P2Y receptor family member 8 | Yp11.2 | P2yr4 (chr X) | A PAR1 gene encoding a member of the family of G-protein coupled receptors. P2RY8 is frequently mutated in germinal-centre B cell-like diffuse large B cell lymphoma (GCB-DLBCL) and Burkitt lymphoma |
8227 | AKAP17A | A-kinase anchoring protein 17A | Yp11.2 | A PAR1 gene encoding a protein kinase A anchoring protein of the spliceosome complex, involved in the regulation of alternate splicing in some mRNA precursors | |
438 | ASMT | Acetylserotonin O-methyltransferase | Yp11.2 | Asmt (chr Y, X) | A PAR1 gene encoding a member of the methyltransferase superfamily, involved in the final reaction in the synthesis of melatonin and meantonin-associated pathophysiology |
207063 | DHRSX | Dehydrogenase/reductase X-linked | Yp11.2 | Dhrsx (chr 4) | A PAR1 gene encoding a non-classical secretary protein, associated with starvation induced autophagy |
9189 | ZBED1 | Zinc finger BED-type containing 1 | Yp11.2 | A PAR1 gene encoding a nucleus protein, likely involved in regulating genes related to cell proliferation, highly expressed in gastric cancer | |
4267 | CD99 | CD99 molecule (Xg blood group) | Yp11.2 | Cd99 (chr 4) | A PAR1 green encoding a cell surface glycoprotein involved in leukocyte migration, T-cell adhesion, ganglioside GM1 and transmembrane protein transport, and T-cell death by a caspase-independent pathway; associated with solitary firous tumor |
6736 | SRY | Sex determining region Y | Yp11.2 | Sry (chr Y) | A MSY intronless gene encoding a protein harboring a high mobility group (HMG)-box, and is the founder of the SRY-box (SOX) family of transcription factors. SRY is the testis-determining factor (TDF), responsible for male sex determination during embryogenesis |
6192 | RPS4Y1 | Ribosomal protein S4, Y-linked 1 | Yp11.2 | Rps4x (chr X) | A MSY gene encoding the ribosomal protein S4, a component of the 40S ribosomal subunit; upregulation could be associated with Parkinson’s disease and schizophrenia |
7544 | ZFY | Zinc finger protein, Y-linked | Yp11.2 | Zfy1/Zhy2 (chr Y) | A MSY gene encoding a zinc finger transcription factor, likely involved in regulation of male germ cell differentiation |
90655 | TGIF2LY | TGFB induced factor homeobox 2 like Y-linked | Yp11.2 | Tgif2lx1 (chr X) | A MSY gene encoding a member of the TALE/TGIF homeobox family of transcription factors, potential regulator of its X homologue |
83259 | PCDH11Y | Protocadherin 11 Y-linked | Yp11.2 | Pcdh11x (chr X) | A MSY gene encoding a member of the protocadherin family, harboring an extracellular domain containing seven cadherin repeats, a transmembrane domain, and a cytoplasmic tail different from those of the classical cadherins, likely involved in cell-cell recognition and cerebral asymmetry during development of the central nervous system |
7258 | TSPY1 | Testis specific protein, Y-linked | Yp11.2 | Tspy-ps (pseudogene) (chr Y) | A testis-specific repetitive MSY gene encoding a protein harboring a SET/NAP domain, involved in binding to cyclin B-CDK1 complex, likely involved in spermatogonial germ cell renewal and male meiotic division. TSPY is a proto-oncogene for the gonadoblastoma locus on the Y chromosome (GBY), promoting cell proliferation. A X-located homologue, TSPX, possesses contrasting functions in cell cycle regulation and serves as a tumor suppressor |
266 | AMELY | Amelogenin, Y-linked | Yp11.2 | Amelx (chr X) | A MSY gene encoding a member of the amelogenin family of extracellular matrix proteins, involved in biomineralization during tooth enamel development |
90665 | TBL1Y | Transducin beta like 1 Y-linked | Yp11.2 | Tbl1x (Chr X) | A MSY gene encoding a member of the WD40 repeat-containing protein family, mediating protein–protein interactions, involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, and cytoskeletal assembly; mutations associated with deafness and coarctation of the aorta |
8287 | USP9Y | Ubiquitin specific peptidase 9, Y-linked | Yq11.221 | Usp9y (chr Y) | A MSY gene and a member of the peptidase C19 family encoding a protein similar to ubiquitin-specific proteases, involved in cleavage of the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins |
8653 | DDX3Y | DEAD-box helicase 3, Y-linked | Yq11.221 | Ddx3y (chr Y) | A MSY gene and a member of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family, involved in ATP binding, hydrolysis, RNA binding, and in the formation of intramolecular interactions; upregulation could be associated with Parkinson’s disease and schizophrenia |
7404 | UTY | Ubiquitously transcribed tetratricopeptide repeat containing, Y-linked | Yq11.221 | Uty (chr Y) | A MSY gene encoding a protein containing tetratricopeptide repeats and homologous to an X-located lysine demethylase 6A (KDM6A), involved in modification of the lysine residues of histone H3; a candidate for the H-Y histocompatibility antigen, involved in graft rejection of male stem cells |
9087 | TMSB4Y | Thymosin beta 4, Y-linked | Yq11.221 | Tmsb4x (chr X) | A MSY gene encoding an actin sequestering protein; likely a tumor suppressor in male breast cancer |
9084 | VCY | Variable charge Y-linked | Yq11.221 | A MSY gene and a member of a family of human VCX/Y repetitive genes, specifically expressed in the testis with unknown functions | |
22829 | NLGN4Y | Neuroligin 4, Y-linked | Yq11.221 | Nlgn3 (chr X) | A MSY gene encoding a type I membrane protein and a member of the neuroligin family, which are cell adhesion molecules present at the postsynaptic side of the synapse and essential for the formation of functional synapses; could be associated with phenotypes of autism spectrum disorder |
86614 | HSFY1 | Heat shock transcription factor, Y-linked 1 | Yq11.222 | Hsf2 (chr 10) | A double-copy MSY gene encoding a member of the heat shock factor (HSF) family of transcriptional activators for heat shock proteins |
9083 | BPY2 | Basic charge Y-linked 2 | Yq11.223 | A MSY repetitive gene expressed specifically in testis. The encoded protein interacts with ubiquitin protein ligase E3A, involved in male germ cell development and male infertility | |
8284 | KDM5D | Lysine demethylase 5D | Yq11.223 | Kdm5d (chr Y) | A MSY gene encoding a histone demethylase containing zinc finger domains, a candidate for the H-Y antigen; involved in neurodevelopment, cardiovascular development and disease and various cancers |
9086 | EIF1AY | Eukaryotic translation initiation factor 1A, Y-linked | Yq11.223 | Eif1a (chr 18) | A MSY gene encoding a protein related to eukaryotic translation initiation factor 1A (EIF1A), associated with dilated ischemic cardiomyopathy and infertility |
5940 | RBMY1A1 | RNA binding motif protein, Y-linked, family 1, multiple members | Yq11.223 | Rbmy (chr Y) | A testis-specific and multiple-copy MSY gene encoding a protein containing an RNA-binding motif in the N-terminus and four SRGY (serine, arginine, glycine, tyrosine) boxes in the C-terminus, involved in RNA splicing regulation during spermatogenesis; aberrantly expressed in liver and other cancers |
9081 | PRY2 | PTPN13 like Y-linked 2 | Yq11.223 | Ptpn13 (chr 5) | A testis-specific MSY gene encoding a protein with a low similarity to protein tyrosine phosphatase, non-receptor type 13; could be involved in apoptosis |
1617 | DAZ1 | Deleted in azoospermia 1 | Yq11.223 | Dazl (chr 17) | A multiple-copy MSY gene encoding an RNA-binding protein important for spermatogenesis. Microdeletion of gene clusters could be involved in infertility in men |
9085 | CDY1 | Chromodomain Y-linked 2A | Yq11.23 | Cdyl (chr 13) | A multiple-copy MSY gene encoding a protein containing a chromodomain and a histone acetyltransferase catalytic domain; involved in germ cell biology and infertility |
10251 | SPRY3 | Sprouty RTK signaling antagonist 3 | Yq12 | Spry3 (chr X) | A PAR2 gene, potentially involved in neurogenesis and pathogenesis of autism |
6845 | VAMP7 | Vesicle associated membrane protein 7 | Yq12 | Vamp7 (chr X) | A PAR2 gene encoding a transmembrane protein and a member of the soluble N-ethylmaleimidesensitive factor attachment protein receptor (SNARE) family, involved in fusion of transport vesicles to target members in endosomes and lysosomes |
3581 | IL9R | Interleukin 9 receptor | Yq12 | Il9r (chr 11) | A gene located at the most terminus of PAR2, associated with asthma pathogenesis. It encodes a cytokine receptor for interleukin 9 (IL9), involved in JAK kinases and STAT proteins functions; could be involved in immune functions, multiphe scherosis and preeclampsia |
Non-functional gene/pseudogenes on the human Y chromosome | |||||
5616 | PRKY | Protein kinase Y-linked pseudogene | Yp11.2 | A MSY pseudogene similar to the protein kinase X-linked on the PAR1 of the X chromosome, with detectable transcripts in various tissues | |
9082 | XKRY | XK related, Y-linked | Yq11.222 | A MSY gene encoding a putative memberane transport protein similar to X-linked Kell blood group. Minimal detectable transcripts in any tissues examined so far, hence its functionality is uncertain | |
146126 | TXLNGY | Taxilin gamma pseudogene, Y-linked | Yq11.222-Yq11.223 | A MSY pseudogene with broad transcript expression in various tissues | |