ZNF311

Summary

ZNF311 (zinc finger protein 311, HGNC:13847) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger protein 311 (Q5JNZ3). May be involved in transcriptional regulation.

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. Predicted to be active in nucleus.

Source: NCBI Gene 282890 — RefSeq curated summary.

At a glance

• GWAS associations: 29
• Clinical variants (ClinVar): 85 total
• MANE Select transcript: NM_001382360

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13847
Approved symbol	ZNF311
Name	zinc finger protein 311
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197935
Ensembl biotype	protein_coding
Entrez	282890

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 21 protein_coding, 1 retained_intron

ENST00000377179, ENST00000483450, ENST00000910907, ENST00000910908, ENST00000910909, ENST00000910910, ENST00000910911, ENST00000910912, ENST00000916441, ENST00000916442, ENST00000916443, ENST00000916444, ENST00000916445, ENST00000916446, ENST00000916447, ENST00000916448, ENST00000916449, ENST00000953056, ENST00000953057, ENST00000953058, ENST00000953059, ENST00000953060

RefSeq mRNA: 3 — MANE Select: NM_001382360 NM_001010877, NM_001350637, NM_001382360

CCDS: CCDS34357

Canonical transcript exons

ENST00000377179 — 7 exons

Exon	Start	End
ENSE00001613743	28999487	28999613
ENSE00001727923	29005008	29005315
ENSE00001767519	28999956	29000047
ENSE00001804643	29003946	29004214
ENSE00003493883	28998734	28998838
ENSE00003537019	28994788	28996586
ENSE00003563990	29003513	29003594

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 88.36.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0699 / max 29.2694, expressed in 612 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72445	0.5493	302
72446	0.5206	292

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.88	gold quality
cortical plate	UBERON:0005343	76.29	gold quality
ventricular zone	UBERON:0003053	75.43	gold quality
ganglionic eminence	UBERON:0004023	75.20	gold quality
right uterine tube	UBERON:0001302	69.63	gold quality
rectum	UBERON:0001052	68.15	gold quality
right lobe of thyroid gland	UBERON:0001119	67.20	gold quality
endometrium	UBERON:0001295	66.99	gold quality
tibial nerve	UBERON:0001323	66.60	gold quality
mucosa of transverse colon	UBERON:0004991	66.22	gold quality
ovary	UBERON:0000992	66.18	gold quality
thyroid gland	UBERON:0002046	66.16	gold quality
right ovary	UBERON:0002118	66.13	gold quality
left lobe of thyroid gland	UBERON:0001120	65.97	gold quality
smooth muscle tissue	UBERON:0001135	65.82	gold quality
left ovary	UBERON:0002119	65.79	gold quality
right testis	UBERON:0004534	65.33	gold quality
testis	UBERON:0000473	65.08	gold quality
fallopian tube	UBERON:0003889	65.03	gold quality
stromal cell of endometrium	CL:0002255	64.49	gold quality
prostate gland	UBERON:0002367	64.04	gold quality
left testis	UBERON:0004533	63.96	gold quality
transverse colon	UBERON:0001157	63.77	gold quality
cortex of kidney	UBERON:0001225	63.65	gold quality
ectocervix	UBERON:0012249	63.41	gold quality
left coronary artery	UBERON:0001626	63.36	gold quality
thoracic mammary gland	UBERON:0005200	63.30	gold quality
colonic epithelium	UBERON:0000397	63.23	silver quality
muscle layer of sigmoid colon	UBERON:0035805	63.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

50 targeting ZNF311, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-2110	99.96	66.68	1930
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481

Literature-anchored findings (GeneRIF, showing 1)

• Prognostic Biomarker ZNF311 and Its Correlation With Tumor Progression and Immune Infiltrates in Glioma. (PMID:33746099)

Cross-species orthologs

0 orthologs

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), ZNF317 (ENSG00000130803), 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)

Protein

Protein identifiers

Zinc finger protein 311 — Q5JNZ3 (reviewed: Q5JNZ3)

Alternative names: Zinc finger protein zfp-31

All UniProt accessions (2): A0A1U9X8W3, Q5JNZ3

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

RefSeq proteins (3): NP_001010877, NP_001337566, NP_001369289* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050826	Krueppel_C2H2_ZnFinger	Family

Pfam: PF00096, PF01352, PF13912

UniProt features (18 total): zinc finger region 14, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JNZ3-F1	65.02	0.11

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 26 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, SNIP1_TARGET_GENES, MIR3606_5P, MIR3129_3P, MIR5583_5P, AHRR_TARGET_GENES, DESCARTES_MAIN_FETAL_PDE1C_ACSM3_POSITIVE_CELLS, BRCA2_TARGET_GENES, HE_LIM_SUN_FETAL_LUNG_C7_PROLIFERATING_SCHWANN_CELL, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, PULVER_FOREY_CELLCYCLE_PEAKING_S1

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): 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), metal ion binding (GO:0046872)

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

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF311	EBLN2	Q6P2I7	595
ZNF311	OR2B3	O76000	580
ZNF311	OR12D3	Q9UGF7	579
ZNF311	PHAF1	Q9BSU1	570
ZNF311	OR2H2	O95918	553
ZNF311	OR2W1	Q9Y3N9	525
ZNF311	TEDC2	Q7L2K0	505
ZNF311	CCDC185	Q8N715	447
ZNF311	OR14J1	Q9UGF5	447
ZNF311	ARHGAP36	Q6ZRI8	418
ZNF311	ACYP2	P14621	418
ZNF311	OR2J2	O76002	402
ZNF311	MUC22	E2RYF6	397
ZNF311	GNL1	P36915	390
ZNF311	MICB	P79525	386

IntAct

5 interactions, top by confidence:

A	B	Type	Score
ZNF311	CENPB	psi-mi:“MI:0914”(association)	0.530
GRB2	ZNF311	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (13): NKTR (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), CENPB (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), CENPB (Affinity Capture-MS), TRIM39 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), CARKD (Affinity Capture-MS), NKTR (Affinity Capture-MS), ZNF311 (Affinity Capture-MS), ZNF311 (Affinity Capture-MS), ZNF311 (Cross-Linking-MS (XL-MS)), ZNF311 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1YEP8, A1YEV9, A1YFW2, A1YG26, A1YG48, A1YG60, A2T6E3, A2T6V8, A2T712, A2T736, A2T7D2, A2T7F4, A2T7L7, A2T812, A6QNZ0, O14709, O15535, O43296, O43309, P10073, P17023, P17097, P49910, Q07231, Q12901, Q15776, Q16670, Q1LZ87, Q3MJ62, Q53GI3, Q571J5, Q5JNZ3, Q5RAE6, Q5RBX0, Q5RCD9, Q5RJ54, Q7Z7L9, Q86W11, Q8IZ26, Q8NF99

Diamond homologs: A1L1L7, A3KN32, A3KN36, A6NFI3, A6NM28, A6NN14, A6QLU5, A7MBI1, A8K8V0, A8MTY0, A8MWA4, B4DU55, C9JBD0, G3X9G7, O60765, O75290, O94892, O95780, P0C7X2, P10072, P15622, P16373, P16374, P17023, P17032, P17097, P17098, P21506, P52742, P59923, Q06730, Q08DG8, Q16587, Q29RZ4, Q2TL60, Q3V080, Q49AA0, Q4R6C2, Q4V8A8, Q5FWF6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1216 predictions. Top by Δscore:

Variant	Effect	Δscore
6:28996587:C:CC	acceptor_gain	1.0000
6:28996588:T:C	acceptor_gain	1.0000
6:28998801:C:CT	acceptor_gain	1.0000
6:28999950:G:C	donor_gain	1.0000
6:28999954:A:AC	donor_gain	1.0000
6:28999955:C:CC	donor_gain	1.0000
6:29003463:CTA:C	donor_gain	1.0000
6:29003518:T:A	donor_gain	1.0000
6:28996585:CA:C	acceptor_gain	0.9900
6:29003462:A:AC	donor_gain	0.9900
6:29003463:C:CC	donor_gain	0.9900
6:29003474:G:C	donor_gain	0.9900
6:29003512:CCG:C	donor_gain	0.9900
6:28998729:CTCA:C	donor_loss	0.9800
6:28998730:TCACC:T	donor_loss	0.9800
6:28998731:CACC:C	donor_loss	0.9800
6:28998732:A:T	donor_loss	0.9800
6:28998802:A:T	acceptor_gain	0.9800
6:28998839:C:CC	acceptor_gain	0.9800
6:28998843:T:TC	acceptor_gain	0.9800
6:29003594:CCTAT:C	acceptor_gain	0.9800
6:28996588:T:TC	acceptor_gain	0.9700
6:28998728:ACT:A	donor_loss	0.9700
6:28998801:C:T	acceptor_gain	0.9700
6:28998846:C:CT	acceptor_gain	0.9700
6:28999981:T:C	donor_gain	0.9700
6:29000043:TAGAG:T	acceptor_gain	0.9700
6:29003463:C:CT	donor_gain	0.9700
6:29003463:CTACA:C	donor_gain	0.9700
6:29003464:T:TT	donor_gain	0.9700

AlphaMissense

4453 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:28995142:A:C	F620L	0.998
6:28995142:A:T	F620L	0.998
6:28995144:A:G	F620L	0.998
6:28995226:G:C	F592L	0.997
6:28995226:G:T	F592L	0.997
6:28995228:A:G	F592L	0.997
6:28995394:G:C	F536L	0.997
6:28995394:G:T	F536L	0.997
6:28995396:A:G	F536L	0.997
6:28995310:G:C	F564L	0.996
6:28995310:G:T	F564L	0.996
6:28995312:A:G	F564L	0.996
6:28995730:G:C	F424L	0.995
6:28995730:G:T	F424L	0.995
6:28995732:A:G	F424L	0.995
6:28995814:G:C	F396L	0.995
6:28995814:G:T	F396L	0.995
6:28995816:A:G	F396L	0.995
6:28995478:G:C	F508L	0.994
6:28995478:G:T	F508L	0.994
6:28995480:A:G	F508L	0.994
6:28996066:G:C	F312L	0.994
6:28996066:G:T	F312L	0.994
6:28996068:A:G	F312L	0.994
6:28995898:G:C	F368L	0.993
6:28995898:G:T	F368L	0.993
6:28995900:A:G	F368L	0.993
6:28995982:G:C	F340L	0.992
6:28995982:G:T	F340L	0.992
6:28995984:A:G	F340L	0.992

dbSNP variants (sampled 300 via entrez): RS1000085829 (6:29003780 A>G,T), RS1000486984 (6:29007350 G>A,T), RS1000509969 (6:28997729 G>T), RS1000871080 (6:29001584 T>G), RS1000975135 (6:29002353 T>G), RS1001492772 (6:29005430 C>T), RS1001584159 (6:29003373 T>A,C), RS1001843809 (6:29004593 AT>A), RS1002034358 (6:28997037 C>T), RS1002550687 (6:29001670 A>G), RS1002853313 (6:29005186 C>T), RS1002963513 (6:28998220 G>A), RS1003220599 (6:29006375 G>C), RS1003291870 (6:29004920 T>C), RS1003301918 (6:28999819 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

29 associations (top):

Study	Trait	p-value
GCST002194_1	Social communication problems	3.000000e-07
GCST003518_58	Daytime sleep phenotypes	1.000000e-06
GCST004521_112	Autism spectrum disorder or schizophrenia	3.000000e-26
GCST004521_212	Autism spectrum disorder or schizophrenia	5.000000e-14
GCST004521_43	Autism spectrum disorder or schizophrenia	2.000000e-27
GCST004521_56	Autism spectrum disorder or schizophrenia	1.000000e-22
GCST004521_58	Autism spectrum disorder or schizophrenia	1.000000e-17
GCST004521_7	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST004521_84	Autism spectrum disorder or schizophrenia	1.000000e-12
GCST004521_91	Autism spectrum disorder or schizophrenia	1.000000e-11
GCST004748_94	Lung cancer	3.000000e-12
GCST004749_79	Lung cancer in ever smokers	9.000000e-08
GCST004750_44	Squamous cell lung carcinoma	4.000000e-11
GCST004866_25	Alopecia areata	9.000000e-07
GCST006101_3	Cardiometabolic and hematological traits	3.000000e-26
GCST007201_360	Schizophrenia	1.000000e-25
GCST008839_516	Height	7.000000e-07
GCST008916_89	Asthma	2.000000e-10
GCST008921_4	Asthma and major depressive disorder	2.000000e-11
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010242_402	HDL cholesterol levels	2.000000e-20
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0005427	social communication impairment
EFO:0007828	daytime rest measurement
EFO:0008111	diet measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
trichostatin A	increases expression	1
avobenzone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	increases expression	1
Fulvestrant	increases methylation	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Valproic Acid	increases expression	1
Vanadates	increases expression	1
Cadmium Chloride	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_XW32	HEK293 eGFP-ZNF311	Transformed cell line	Female

Clinical trials (associated diseases)

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