ZNF317

gene
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Summary

ZNF317 (zinc finger protein 317, HGNC:13507) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 317 (Q96PQ6). May function as a transcription factor. It is a selective cancer dependency (DepMap: 10.8% of cell lines).

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleus.

Source: NCBI Gene 57693 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 98 total
  • Cancer dependency (DepMap): dependent in 10.8% of screened cell lines
  • MANE Select transcript: NM_020933

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13507
Approved symbolZNF317
Namezinc finger protein 317
Location19p13.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000130803
Ensembl biotypeprotein_coding
OMIM613864
Entrez57693

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000247956, ENST00000360385, ENST00000419608, ENST00000590152, ENST00000591278, ENST00000591508, ENST00000891822, ENST00000891823, ENST00000933872, ENST00000933873, ENST00000933874, ENST00000933875, ENST00000933876, ENST00000949134, ENST00000949135, ENST00000949136

RefSeq mRNA: 2 — MANE Select: NM_020933 NM_001190791, NM_020933

CCDS: CCDS12210, CCDS54213

Canonical transcript exons

ENST00000247956 — 7 exons

ExonStartEnd
ENSE0000134551191559259156041
ENSE0000168383691572689157394
ENSE0000275469091403979140592
ENSE0000287466891601149163413
ENSE0000356100791566129156748
ENSE0000368656891588269158908
ENSE0000368850691579809158075

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 90.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.2788 / max 124.1033, expressed in 1816 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
17369210.32391791
1736919.95491792

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009490.84gold quality
cardiac muscle of right atriumUBERON:000337990.40silver quality
upper arm skinUBERON:000426390.11gold quality
left ventricle myocardiumUBERON:000656689.96silver quality
kidney epitheliumUBERON:000481989.66silver quality
mucosa of transverse colonUBERON:000499189.54gold quality
ileal mucosaUBERON:000033189.17gold quality
cortical plateUBERON:000534389.15gold quality
lower esophagus mucosaUBERON:003583488.36gold quality
embryoUBERON:000092287.76gold quality
ganglionic eminenceUBERON:000402387.76gold quality
ventricular zoneUBERON:000305387.75gold quality
islet of LangerhansUBERON:000000687.17gold quality
skin of abdomenUBERON:000141686.75gold quality
spleenUBERON:000210686.56gold quality
apex of heartUBERON:000209886.48gold quality
skin of legUBERON:000151186.31gold quality
leukocyteCL:000073886.21gold quality
monocyteCL:000057685.82gold quality
zone of skinUBERON:000001485.64gold quality
olfactory segment of nasal mucosaUBERON:000538685.06gold quality
pancreasUBERON:000126485.03gold quality
right lobe of liverUBERON:000111485.00gold quality
muscle layer of sigmoid colonUBERON:003580584.99gold quality
lower esophagusUBERON:001347384.94gold quality
lower esophagus muscularis layerUBERON:003583384.93gold quality
small intestine Peyer’s patchUBERON:000345484.63gold quality
adenohypophysisUBERON:000219684.57gold quality
body of pancreasUBERON:000115084.47gold quality
body of stomachUBERON:000116184.46gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no3.18

Regulation

Is transcription factor: yes

JASPAR motifs

MotifNameFamily
MA1593.1ZNF317More than 3 adjacent zinc fingers
MA1593.2ZNF317More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28273063

miRNA regulators (miRDB)

46 targeting ZNF317, 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-6873-3P100.0071.422626
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-4283100.0066.422097
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-428299.9975.366408
HSA-MIR-453499.9966.581907
HSA-MIR-806899.9873.852376
HSA-MIR-808299.9567.271170
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-335-3P99.9373.364958
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-629-3P99.8567.991875
HSA-MIR-383-3P99.8565.841359
HSA-MIR-129999.7771.242389
HSA-MIR-432099.7565.80793
HSA-MIR-808499.7369.571760
HSA-MIR-432899.5771.064094
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-6740-3P99.4868.491392
HSA-MIR-766-5P99.4767.912225
HSA-MIR-391599.4568.491905
HSA-MIR-65099.4565.771309
HSA-MIR-425199.4069.193363
HSA-MIR-6882-5P99.3571.131206
HSA-MIR-569399.2466.671106
HSA-MIR-607199.1667.771780
HSA-MIR-323B-3P99.1468.89725
HSA-MIR-19898.7067.32920
HSA-MIR-797798.6566.182590

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 10.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • molecular cloning and characterization of isoforms (PMID:11688974)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZfp317ENSMUSG00000057551
rattus_norvegicusZfp317ENSRNOG00000006684

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 317Q96PQ6 (reviewed: Q96PQ6)

All UniProt accessions (3): Q96PQ6, K7EKT9, K7ERD6

UniProt curated annotations — full annotation on UniProt →

Function. May function as a transcription factor. May play an important role in erythroid maturation and lymphoid proliferation.

Subcellular location. Nucleus.

Tissue specificity. Isoform 1 and isoform 2 are ubiquitously expressed. Isoform 3 and isoform 4 are expressed only in lymphocytes, spleen and lung.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (4)

UniProt IDNamesCanonical?
Q96PQ6-12, ZNF317-2yes
Q96PQ6-21, ZNF317-1
Q96PQ6-33, ZNF317-3
Q96PQ6-44, ZNF317-4

RefSeq proteins (2): NP_001177720, NP_065984* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR050752C2H2-ZF_domainFamily

Pfam: PF00096, PF01352

UniProt features (20 total): zinc finger region 13, splice variant 2, chain 1, domain 1, region of interest 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96PQ6-F168.100.05

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-212436Generic Transcription Pathway
R-HSA-9843940Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 74 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, SENESE_HDAC1_TARGETS_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GCM_DENR, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
RNA Polymerase II Transcription1
Regulation of endogenous retroelements1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II2
transcription by RNA polymerase II2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
negative regulation of DNA-templated transcription1
regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
transition metal ion binding1
nucleic acid binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF317OR4N4CA0A096LPK9507
ZNF317CARM1Q86X55488
ZNF317CNDP2Q96KP4393
ZNF317PRR12Q9ULL5377
ZNF317GTF3C5Q9Y5Q8375
ZNF317DNAJC5GQ8N7S2355
ZNF317CTPS2Q9NRF8352
ZNF317DHX15O43143298
ZNF317STX16O14662286
ZNF317SETD5Q9C0A6270
ZNF317ATMINO43313263
ZNF317TOP1P11387258
ZNF317KCNAB2Q13303253
ZNF317TRIM28Q13263249
ZNF317PRMT2P55345242

IntAct

89 interactions, top by confidence:

ABTypeScore
NKAPD1ZNF317psi-mi:“MI:0915”(physical association)0.780
ZNF317NKAPD1psi-mi:“MI:0915”(physical association)0.780
ZNF317RBMY1A1psi-mi:“MI:0915”(physical association)0.740
RBMY1A1ZNF317psi-mi:“MI:0915”(physical association)0.740
AENZNF317psi-mi:“MI:0915”(physical association)0.670
ZNF317AENpsi-mi:“MI:0915”(physical association)0.670
ZNF837ZNF317psi-mi:“MI:0915”(physical association)0.560
RBMY1FZNF317psi-mi:“MI:0915”(physical association)0.560
RBM10ZNF317psi-mi:“MI:0915”(physical association)0.560
RBMY1A1ZNF317psi-mi:“MI:0915”(physical association)0.560
ZNF317ZNF408psi-mi:“MI:0915”(physical association)0.560
ZNF317CIB3psi-mi:“MI:0915”(physical association)0.560
ZNF524ZNF317psi-mi:“MI:0915”(physical association)0.560
CLK2ZNF317psi-mi:“MI:0915”(physical association)0.560
ZBTB48ZNF317psi-mi:“MI:0915”(physical association)0.560
ZNF648ZNF317psi-mi:“MI:0915”(physical association)0.560
BAHD1ZNF317psi-mi:“MI:0915”(physical association)0.560
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
RSBN1SETD1Apsi-mi:“MI:0914”(association)0.530
PPANPPM1Gpsi-mi:“MI:0914”(association)0.530

BioGRID (93): ZNF317 (Two-hybrid), ZNF317 (Two-hybrid), AEN (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-9 (Two-hybrid), RPL26L1 (Affinity Capture-MS), RPL26 (Affinity Capture-MS), RPS3A (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), TUBA8 (Affinity Capture-MS), RPL13 (Affinity Capture-MS), MRPS18A (Affinity Capture-MS), RBMY1A1 (Two-hybrid), TUBA8 (Affinity Capture-MS), ZNF317 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A6QLU5, B2RUI1, D3ZVT0, O14709, O43296, O75123, P10072, P15621, P17020, P17097, P51814, P85977, Q08ER8, Q0VGE8, Q14590, Q32KN0, Q3KQV3, Q4V8A8, Q5CZA5, Q5RBX0, Q5RCD9, Q5VIY5, Q61116, Q61967, Q6GQR8, Q6P9A3, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q86UD4, Q86WZ6, Q8BFS8, Q8IZ26, Q8N9F8, Q8TAF7

Diamond homologs: A0A1W2PQL4, A0JNB1, A0JPL0, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MT65, A8MUV8, A8MWA4, B2RXC5, B4DU55, B4DX44, E9PYI1, O14628, O75346, P0CH99, P0CI00, P17014, P17030, P17032, P17098, P51786, P85977, Q02386, Q06730, Q06732, Q0VAW7, Q12901, Q13360, Q14586, Q14588, Q14590, Q16587, Q2M3X9, Q2VY69, Q32M78, Q3ZCX4, Q49AA0, Q4R6J4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 62 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Peptide chain elongation730.6×7e-08
Viral mRNA Translation730.6×7e-08
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA730.3×7e-08
Selenocysteine synthesis729.0×7e-08
Eukaryotic Translation Termination729.0×7e-08
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)728.4×7e-08
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA728.4×7e-08
SRP-dependent cotranslational protein targeting to membrane827.6×3e-08

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation826.9×1e-07
translation713.1×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance79
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1217 predictions. Top by Δscore:

VariantEffectΔscore
19:9140588:GTCGT:Gdonor_gain1.0000
19:9140591:GT:Gdonor_gain1.0000
19:9140593:G:GGdonor_gain1.0000
19:9143041:A:Tdonor_gain1.0000
19:9157393:GG:Gdonor_gain1.0000
19:9157394:GG:Gdonor_gain1.0000
19:9157394:GGTAA:Gdonor_loss1.0000
19:9157395:G:GAdonor_loss1.0000
19:9157395:G:GGdonor_gain1.0000
19:9158824:A:AGacceptor_gain1.0000
19:9158824:AGATT:Aacceptor_gain1.0000
19:9158825:G:GAacceptor_gain1.0000
19:9158825:GATT:Gacceptor_gain1.0000
19:9158825:GATTG:Gacceptor_gain1.0000
19:9158905:GATG:Gdonor_gain1.0000
19:9158906:ATGGT:Adonor_loss1.0000
19:9158908:GGT:Gdonor_loss1.0000
19:9158909:G:GGdonor_gain1.0000
19:9158909:G:Tdonor_loss1.0000
19:9158910:TAAGA:Tdonor_loss1.0000
19:9140589:TCGT:Tdonor_gain0.9900
19:9140589:TCGTG:Tdonor_loss0.9900
19:9140590:CGTG:Cdonor_loss0.9900
19:9140591:GTGTA:Gdonor_loss0.9900
19:9140593:G:Tdonor_loss0.9900
19:9140594:T:TCdonor_loss0.9900
19:9156735:GT:Gdonor_gain0.9900
19:9156742:TTCCC:Tdonor_gain0.9900
19:9156881:G:GTdonor_gain0.9900
19:9158820:TTTCA:Tacceptor_loss0.9900

AlphaMissense

3979 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:9161260:T:CF539L1.000
19:9161262:C:AF539L1.000
19:9161262:C:GF539L1.000
19:9160336:T:CF231L0.999
19:9160338:C:AF231L0.999
19:9160338:C:GF231L0.999
19:9160420:T:CF259L0.999
19:9160422:C:AF259L0.999
19:9160422:C:GF259L0.999
19:9160672:T:CF343L0.999
19:9160674:C:AF343L0.999
19:9160674:C:GF343L0.999
19:9160756:T:CF371L0.999
19:9160758:C:AF371L0.999
19:9160758:C:GF371L0.999
19:9161008:T:CF455L0.999
19:9161010:C:AF455L0.999
19:9161010:C:GF455L0.999
19:9161210:G:CR522P0.999
19:9161294:G:CR550P0.999
19:9161344:T:CF567L0.999
19:9161346:C:AF567L0.999
19:9161346:C:GF567L0.999
19:9160504:T:CF287L0.998
19:9160506:C:AF287L0.998
19:9160506:C:GF287L0.998
19:9160701:C:AH352Q0.998
19:9160701:C:GH352Q0.998
19:9160924:T:CF427L0.998
19:9160926:C:AF427L0.998

dbSNP variants (sampled 300 via entrez): RS1000307709 (19:9148251 C>T), RS1000470452 (19:9153741 T>C), RS1000595559 (19:9143300 T>G), RS1000667158 (19:9141887 C>T), RS1000700621 (19:9149304 T>G), RS1000708398 (19:9138593 C>A,G), RS1000763855 (19:9138884 T>G), RS1001049821 (19:9143949 T>G), RS1001209288 (19:9155307 C>G), RS1001387537 (19:9153144 TTGTTTTTGTTTG>T), RS1001390777 (19:9139034 G>A), RS1001442905 (19:9153480 G>A), RS1001575779 (19:9161549 G>A), RS1001603147 (19:9138461 G>A), RS1001629552 (19:9161209 C>G,T)

Disease associations

OMIM: gene MIM:613864 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST003542_87Night sleep phenotypes5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
bisphenol Faffects cotreatment, increases expression1
bisphenol Aincreases expression1
arseniteaffects binding, decreases reaction1
sodium arseniteincreases expression1
zinc chromateincreases abundance, increases expression1
chromium hexavalent ionincreases abundance, increases expression1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression, decreases reaction1
Sunitinibincreases expression1
Vehicle Emissionsdecreases expression, decreases reaction1
Dexamethasoneaffects cotreatment, increases expression1
Diurondecreases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Methotrexatedecreases expression1
Methyl Methanesulfonateincreases expression1
Plant Oilsincreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Asbestos, Crocidolitedecreases expression1
Cadmium Chlorideincreases expression1
Particulate Matterdecreases expression, decreases reaction1

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.