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ZFY

gene
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Also known as ZNF911

Summary

ZFY (zinc finger protein Y-linked, HGNC:12870) is a protein-coding gene on chromosome Yp11.2, encoding Zinc finger Y-chromosomal protein (P08048). Probable transcriptional activator.

This gene encodes a zinc finger-containing protein that may function as a transcription factor. This gene was once a candidate gene for the testis-determining factor (TDF) and was erroneously referred to as TDF.

Source: NCBI Gene 7544 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 46 total
  • MANE Select transcript: NM_003411

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12870
Approved symbolZFY
Namezinc finger protein Y-linked
LocationYp11.2
Locus typegene with protein product
StatusApproved
AliasesZNF911
Ensembl geneENSG00000067646
Ensembl biotypeprotein_coding
OMIM490000
Entrez7544

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000155093, ENST00000383052, ENST00000443793, ENST00000449237, ENST00000469869, ENST00000478783, ENST00000625061, ENST00000890804, ENST00000963502

RefSeq mRNA: 12 — MANE Select: NM_003411 NM_001145275, NM_001145276, NM_001369702, NM_001369703, NM_001369704, NM_001369705, NM_001369706, NM_001369707, NM_001369708, NM_001369709, NM_001369710, NM_003411

CCDS: CCDS14774, CCDS48200, CCDS48201

Canonical transcript exons

ENST00000155093 — 8 exons

ExonStartEnd
ENSE0000164858529353812935769
ENSE0000376442129750952975244
ENSE0000376846829755112975654
ENSE0000388948029539092953997
ENSE0000388985929766702976822
ENSE0000389166029779402978080
ENSE0000389570829788102982506
ENSE0000389584829610742961646

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 93.76.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8356 / max 61.8116, expressed in 844 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
2010962.8356844

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001993.76gold quality
male germ cellCL:000001589.98gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.57gold quality
rectumUBERON:000105276.80gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047375.95gold quality
parietal pleuraUBERON:000240075.30gold quality
trabecular bone tissueUBERON:000248374.32gold quality
calcaneal tendonUBERON:000370173.80gold quality
oral cavityUBERON:000016773.58gold quality
adrenal tissueUBERON:001830373.58gold quality
upper leg skinUBERON:000426273.37gold quality
pleuraUBERON:000097772.89gold quality
mucosa of paranasal sinusUBERON:000503072.82gold quality
right lungUBERON:000216771.66gold quality
mucosa of transverse colonUBERON:000499171.12gold quality
amniotic fluidUBERON:000017370.80gold quality
cauda epididymisUBERON:000436070.76gold quality
penisUBERON:000098970.70gold quality
palpebral conjunctivaUBERON:000181270.33gold quality
prostate glandUBERON:000236770.31gold quality
ventricular zoneUBERON:000305370.22gold quality
testisUBERON:000047370.14gold quality
endothelial cellCL:000011570.11silver quality
corpus epididymisUBERON:000435970.08gold quality
superficial temporal arteryUBERON:000161470.01gold quality
metanephros cortexUBERON:001053369.66gold quality
visceral pleuraUBERON:000240169.45gold quality
left testisUBERON:000453369.28gold quality
caput epididymisUBERON:000435869.24gold quality
right testisUBERON:000453469.07gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

116 targeting ZFY, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-5692A100.0074.406850
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3646100.0073.565283
HSA-MIR-1193100.0065.93529
HSA-MIR-4533100.0069.482758
HSA-MIR-428299.9975.366408
HSA-MIR-186-5P99.9970.833707
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-477599.9875.006394
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-590-3P99.9674.346478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-381-3P99.9371.872854
HSA-MIR-4760-3P99.9370.502385

Literature-anchored findings (GeneRIF, showing 2)

  • Studies identified a major testis-specific ZFY transcript that encodes a protein with the same short acidic domain. (PMID:22407129)
  • Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters. (PMID:32406922)

Cross-species orthologs

0 orthologs

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger Y-chromosomal protein — P08048 (reviewed: P08048)

All UniProt accessions (2): P08048, C9JQM1

UniProt curated annotations — full annotation on UniProt →

Function. Probable transcriptional activator. Binds to the consensus sequence 5’-AGGCCY-3'.

Subcellular location. Nucleus.

Domain organisation. The binding of ZFY to DNA is mediated by the interaction of the GGCC core base pairs with zinc fingers 12 and 13.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family. ZFX/ZFY subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
P08048-11yes
P08048-22
P08048-33

RefSeq proteins (12): NP_001138747, NP_001138748, NP_001356631, NP_001356632, NP_001356633, NP_001356634, NP_001356635, NP_001356636, NP_001356637, NP_001356638, NP_001356639, NP_003402* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006794Transcrp_activ_Zfx/Zfy-domDomain
IPR013087Znf_C2H2_typeDomain
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF04704, PF13909

UniProt features (29 total): zinc finger region 13, sequence conflict 6, splice variant 5, strand 2, chain 1, modified residue 1, helix 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
1KLRSOLUTION NMR
1KLSSOLUTION NMR
1XRZSOLUTION NMR
5ZNFSOLUTION NMR
7ZNFSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P08048-F154.230.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 270

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 127 (showing top): GOBP_BEHAVIOR, CCAWYNNGAAR_UNKNOWN, XU_GH1_AUTOCRINE_TARGETS_UP, SP3_Q3, GOBP_GROWTH, GOBP_OOGENESIS, CREBP1_Q2, BROWNE_HCMV_INFECTION_16HR_UP, GOBP_MALE_GAMETE_GENERATION, BROWNE_HCMV_INFECTION_12HR_UP, YY1_Q6, GOBP_OVARIAN_FOLLICLE_DEVELOPMENT, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT, YY1_02, GOBP_PARENTAL_BEHAVIOR

GO Biological Process (12): ovarian follicle development (GO:0001541), regulation of transcription by RNA polymerase II (GO:0006357), spermatogenesis (GO:0007283), fertilization (GO:0009566), post-embryonic development (GO:0009791), multicellular organism growth (GO:0035264), positive regulation of transcription by RNA polymerase II (GO:0045944), oocyte development (GO:0048599), homeostasis of number of cells (GO:0048872), parental behavior (GO:0060746), regulation of DNA-templated transcription (GO:0006355), germ cell development (GO:0007281)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), zinc ion binding (GO:0008270), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
transcription by RNA polymerase II2
developmental process involved in reproduction2
multicellular organismal process2
regulation of transcription by RNA polymerase II2
cellular anatomical structure2
nuclear lumen2
female gonad development1
anatomical structure development1
regulation of DNA-templated transcription1
male gamete generation1
sexual reproduction1
reproductive process1
multicellular organism development1
developmental growth1
positive regulation of DNA-templated transcription1
germ cell development1
oocyte differentiation1
multicellular organismal-level homeostasis1
reproductive behavior1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
gamete generation1
cellular process involved in reproduction in multicellular organism1
cell development1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
transition metal ion binding1
DNA binding1
nucleic acid binding1
binding1
cation binding1
chromosome1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1

Protein interactions and networks

STRING

764 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZFYSRYQ05066949
ZFYUSP9YO00507876
ZFYDDX3YO15523876
ZFYKDM5DQ9BY66864
ZFYEIF1AYO14602836
ZFYUTYO14607794
ZFYRPS4Y1P22090786
ZFYAMELYQ99218783
ZFYTMSB4YO14604770
ZFYNLGN4YQ8NFZ3752
ZFYTSPY1P09002747
ZFYAMELXQ99217736
ZFYMEA1Q16626716
ZFYZPR1O75312702
ZFYPRKYO43930681

IntAct

21 interactions, top by confidence:

ABTypeScore
L3MBTL2ZFYpsi-mi:“MI:0915”(physical association)0.720
ZFYL3MBTL2psi-mi:“MI:0915”(physical association)0.720
ZFYDMRT3psi-mi:“MI:0915”(physical association)0.560
ZFYKAT14psi-mi:“MI:0915”(physical association)0.560
ZFYpsi-mi:“MI:0915”(physical association)0.370
CCL22ZFYpsi-mi:“MI:0915”(physical association)0.370
IL31ZFYpsi-mi:“MI:0915”(physical association)0.370
ZFYZBTB9psi-mi:“MI:0915”(physical association)0.370
ZFYZFXpsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
L3MBTL2ZFYpsi-mi:“MI:0915”(physical association)0.000
DMRT3ZFYpsi-mi:“MI:0915”(physical association)0.000
KAT14ZFYpsi-mi:“MI:0915”(physical association)0.000

BioGRID (16): ZFY (Affinity Capture-MS), ZFX (Affinity Capture-MS), NSD1 (Affinity Capture-MS), CACNB3 (Affinity Capture-MS), ZFY (Two-hybrid), ZFY (Two-hybrid), L3MBTL2 (Two-hybrid), CSRP2BP (Two-hybrid), CACNB3 (Affinity Capture-MS), ZFX (Affinity Capture-MS), NSD1 (Affinity Capture-MS), ZFY (Proximity Label-MS), ZFY (Affinity Capture-MS), PPIB (Cross-Linking-MS (XL-MS)), ZFY (Affinity Capture-RNA)

ESM2 similar proteins: A1L1J6, A2ANX9, A7Y7X5, E9Q8T2, G5E8B9, O15060, O43167, O43829, O62836, O95625, P08048, P0C6P6, P10925, P17010, P17012, P20662, P52739, Q01611, Q08376, Q0VCB0, Q2FAY8, Q3TTC2, Q4V8R6, Q52V16, Q5DU09, Q5PPG4, Q5R5M1, Q5R5N5, Q5RAU9, Q5SVQ8, Q6B4Z5, Q6GNP2, Q6INV8, Q7TS63, Q7ZVR6, Q80V63, Q80X44, Q811F1, Q8K3J5, Q92010

Diamond homologs: A0A9P4XV22, A2ANX9, B1H2Q6, O62836, P08048, P0CJ78, P10925, P17010, P17012, P20662, P27705, P28698, P52288, P80944, Q01611, Q03081, Q03125, Q0VDT2, Q29419, Q3U3I9, Q52V16, Q567C6, Q5U2Z0, Q6B4Z5, Q7RTV3, Q95LI3, Q966L8, Q96EG3, Q9UDV6, Q9UL36, Q9Y462, A1L2U9, A2A884, A7Y7X5, B0X9H6, B0YDH7, B1WAZ8, B1WBU4, O35615, O77459

SIGNOR signaling

1 interactions.

AEffectBMechanism
HNRNPU“up-regulates quantity by stabilization”ZFY“post transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

46 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1517 predictions. Top by Δscore:

VariantEffectΔscore
Y:2935442:GTCGG:Gdonor_gain1.0000
Y:2935444:CGGG:Cdonor_loss1.0000
Y:2935445:GG:Gdonor_gain1.0000
Y:2935446:GG:Gdonor_gain1.0000
Y:2935447:G:Cdonor_loss1.0000
Y:2935447:G:GGdonor_gain1.0000
Y:2935448:TGAGT:Tdonor_loss1.0000
Y:2961072:A:Gacceptor_gain1.0000
Y:2961645:GT:Gdonor_gain1.0000
Y:2961647:G:GGdonor_gain1.0000
Y:2975084:T:TAacceptor_gain1.0000
Y:2975090:TTCA:Tacceptor_loss1.0000
Y:2975091:TCA:Tacceptor_loss1.0000
Y:2975092:CAGT:Cacceptor_loss1.0000
Y:2975093:A:ACacceptor_loss1.0000
Y:2975093:A:AGacceptor_gain1.0000
Y:2975093:AGT:Aacceptor_gain1.0000
Y:2975093:AGTG:Aacceptor_gain1.0000
Y:2975094:G:GAacceptor_gain1.0000
Y:2975094:GT:Gacceptor_gain1.0000
Y:2975094:GTG:Gacceptor_gain1.0000
Y:2975094:GTGG:Gacceptor_gain1.0000
Y:2975094:GTGGA:Gacceptor_gain1.0000
Y:2975245:G:Cdonor_loss1.0000
Y:2975245:G:GGdonor_gain1.0000
Y:2975246:T:Gdonor_loss1.0000
Y:2975508:TAGGT:Tacceptor_loss1.0000
Y:2975509:A:AGacceptor_gain1.0000
Y:2975509:A:Tacceptor_loss1.0000
Y:2975510:G:GGacceptor_gain1.0000

AlphaMissense

5423 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
Y:2978854:T:CC423R1.000
Y:2978855:G:AC423Y1.000
Y:2978856:C:GC423W1.000
Y:2978863:T:AC426S1.000
Y:2978863:T:CC426R1.000
Y:2978864:G:AC426Y1.000
Y:2978864:G:CC426S1.000
Y:2978865:T:GC426W1.000
Y:2978875:T:CF430L1.000
Y:2978876:T:CF430S1.000
Y:2978877:T:AF430L1.000
Y:2978877:T:GF430L1.000
Y:2978902:C:GH439D1.000
Y:2978904:C:AH439Q1.000
Y:2978904:C:GH439Q1.000
Y:2979136:T:CC517R1.000
Y:2979145:T:CC520R1.000
Y:2979146:G:AC520Y1.000
Y:2979147:T:GC520W1.000
Y:2979186:C:AH533Q1.000
Y:2979186:C:GH533Q1.000
Y:2979223:T:CC546R1.000
Y:2979224:G:AC546Y1.000
Y:2979225:T:GC546W1.000
Y:2979232:T:CC549R1.000
Y:2979244:T:CF553L1.000
Y:2979245:T:CF553S1.000
Y:2979246:C:AF553L1.000
Y:2979246:C:GF553L1.000
Y:2979263:T:CL559P1.000

dbSNP variants (sampled 300 via entrez): RS1000144147 (Y:2935615 T>C), RS1000260605 (Y:2936577 C>G), RS1000333799 (Y:2939571 G>T), RS1000613335 (Y:2980551 G>A), RS1000767075 (Y:2978717 G>A), RS1001732720 (Y:2967583 G>T), RS1001879229 (Y:2970604 T>C), RS1002543248 (Y:2952322 C>T), RS1002847604 (Y:2968534 C>T), RS1003098404 (Y:2950580 G>A), RS1003545481 (Y:2962314 C>A), RS1004714498 (Y:2962860 G>A), RS1004776802 (Y:2964260 A>G), RS1006386662 (Y:2952716 G>A), RS1006825557 (Y:2973532 G>T)

Disease associations

OMIM: gene MIM:490000 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
Particulate Matterincreases methylation, increases abundance, increases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
bisphenol Aincreases methylation1
arsenitedecreases methylation, increases expression1
sodium arseniteaffects methylation1
butyraldehydedecreases expression1
manganese chloridedecreases expression, increases abundance1
potassium chromate(VI)decreases expression1
pentanaldecreases expression1
abrineincreases expression1
incobotulinumtoxinAdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Panobinostatdecreases expression1
Air Pollutants, Occupationalaffects expression1
Amphotericin Bdecreases expression1
Vehicle Emissionsincreases abundance, increases expression1
Caffeineincreases phosphorylation1
Chromiumdecreases expression1
Clorgylineincreases expression1
Formaldehydedecreases expression1
Hydroxyureaincreases expression1
Manganesedecreases expression, increases abundance1
Plant Extractsaffects cotreatment, increases expression1
Plant Oilsincreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Vanadatesincreases expression1
Vitamin Edecreases expression1
Cyclosporineincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot