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Table 1 Protein-coding genes and functions on the human Y chromosome

From: Y chromosome in health and diseases

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
  1. aAdopted from the National Center for Biotechnology Information (NCBI) and PubMed databases [35]