ZNF90

Summary

ZNF90 (zinc finger protein 90, HGNC:13165) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 90 (Q03938). 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 DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 7643 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 129 total
• Cancer driver (intOGen): activating (oncogene-like) across 1 cancer types
• MANE Select transcript: NM_007138

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13165
Approved symbol	ZNF90
Name	zinc finger protein 90
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	HTF9
Ensembl gene	ENSG00000213988
Ensembl biotype	protein_coding
OMIM	603973
Entrez	7643

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 protein_coding, 1 retained_intron

ENST00000418063, ENST00000469078, ENST00000473524, ENST00000474284, ENST00000484032, ENST00000492328

RefSeq mRNA: 1 — MANE Select: NM_007138 NM_007138

CCDS: CCDS46028

Canonical transcript exons

ENST00000418063 — 4 exons

Exon	Start	End
ENSE00001805619	20117781	20121165
ENSE00001852237	20078000	20078135
ENSE00002532604	20104239	20104365
ENSE00003493161	20105221	20105316

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 85.17.

FANTOM5 (CAGE): breadth broad, TPM avg 6.8900 / max 353.2532, expressed in 900 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174842	6.6303	894
174843	0.2596	101

Top tissues by expression

246 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	85.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.32	gold quality
buccal mucosa cell	CL:0002336	81.91	silver quality
right lobe of thyroid gland	UBERON:0001119	81.87	gold quality
ventricular zone	UBERON:0003053	81.11	gold quality
left lobe of thyroid gland	UBERON:0001120	79.84	gold quality
ganglionic eminence	UBERON:0004023	78.72	gold quality
thyroid gland	UBERON:0002046	78.66	gold quality
right uterine tube	UBERON:0001302	77.01	gold quality
left ovary	UBERON:0002119	75.96	gold quality
right ovary	UBERON:0002118	75.11	gold quality
mucosa of transverse colon	UBERON:0004991	74.19	gold quality
body of uterus	UBERON:0009853	73.78	gold quality
endocervix	UBERON:0000458	73.45	gold quality
adrenal tissue	UBERON:0018303	73.02	gold quality
smooth muscle tissue	UBERON:0001135	72.91	gold quality
body of pancreas	UBERON:0001150	72.77	gold quality
ovary	UBERON:0000992	71.93	gold quality
ectocervix	UBERON:0012249	71.39	gold quality
body of stomach	UBERON:0001161	71.18	gold quality
skin of abdomen	UBERON:0001416	71.15	gold quality
pancreas	UBERON:0001264	70.66	gold quality
calcaneal tendon	UBERON:0003701	70.06	gold quality
left uterine tube	UBERON:0001303	70.01	gold quality
metanephros cortex	UBERON:0010533	70.01	gold quality
cortical plate	UBERON:0005343	69.99	gold quality
stomach	UBERON:0000945	69.75	gold quality
islet of Langerhans	UBERON:0000006	69.67	gold quality
stromal cell of endometrium	CL:0002255	69.66	gold quality
transverse colon	UBERON:0001157	69.38	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.03
E-MTAB-5061	no	1.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting ZNF90, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786

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 90 — Q03938 (reviewed: Q03938)

Alternative names: Zinc finger protein HTF9

All UniProt accessions (3): Q03938, F8WBQ5, F8WDJ7

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 (1): NP_009069* (*=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

Pfam: PF00096, PF01352

UniProt features (17 total): zinc finger region 15, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q03938-F1	74.24	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): chr19p12, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HSD17B8_TARGET_GENES, SRSF9_TARGET_GENES, MIR23A_3P_MIR23B_3P, MIR23C, MIR6809_3P, MIR4753_3P, MIR6833_3P, MIR6873_3P, MIR587, MIR3059_5P, MIR4768_5P, MIR9_3P

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

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), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), metal ion binding (GO:0046872)

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

GO top-level categories

Rollup of top GO terms by namespace:

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

Protein interactions and networks

STRING

332 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF90	M0R233	M0R233	407
ZNF90	ZNG1B	Q8IUF1	400
ZNF90	M0R1X1	M0R1X1	400
ZNF90	KAT8	Q9H7Z6	398
ZNF90	CCDC74B	Q96LY2	378
ZNF90	CNPPD1	Q9BV87	370
ZNF90	UBALD2	Q8IYN6	348
ZNF90	CCDC150	Q8NCX0	348
ZNF90	ZNF438	Q7Z4V0	323
ZNF90	DTD2	Q96FN9	315
ZNF90	ANKRD18A	Q8IVF6	312
ZNF90	THUMPD3	Q9BV44	306
ZNF90	CCDC77	Q9BR77	302
ZNF90	PLPP6	Q8IY26	295
ZNF90	HROB	Q8N3J3	294

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ECE1	ZNF90	psi-mi:“MI:0915”(physical association)	0.370
ZNF90	SETSIP	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): ZNF90 (Affinity Capture-MS), ZNF90 (Affinity Capture-MS), ZNF90 (Cross-Linking-MS (XL-MS)), ZNF90 (Cross-Linking-MS (XL-MS)), ZNF90 (Cross-Linking-MS (XL-MS)), ZNF90 (Affinity Capture-RNA)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 1 cancer types — NPC.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	121
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

896 predictions. Top by Δscore:

Variant	Effect	Δscore
19:20104326:G:T	donor_gain	1.0000
19:20104368:GAGGA:G	donor_gain	1.0000
19:20104371:GA:G	donor_gain	1.0000
19:20104372:A:G	donor_gain	1.0000
19:20117780:GTTAT:G	acceptor_gain	1.0000
19:20078132:AATG:A	donor_loss	0.9900
19:20078133:ATGGT:A	donor_loss	0.9900
19:20078134:TGGTG:T	donor_loss	0.9900
19:20078136:G:A	donor_loss	0.9900
19:20104372:A:AG	donor_gain	0.9900
19:20117779:A:AG	acceptor_gain	0.9900
19:20117780:G:GG	acceptor_gain	0.9900
19:20117780:GTT:G	acceptor_gain	0.9900
19:20078410:G:GT	donor_gain	0.9800
19:20104230:GTTTT:G	acceptor_loss	0.9800
19:20104231:TTTTT:T	acceptor_loss	0.9800
19:20104232:TTTTC:T	acceptor_loss	0.9800
19:20104233:TTTCA:T	acceptor_loss	0.9800
19:20104234:TTCA:T	acceptor_loss	0.9800
19:20104235:TCA:T	acceptor_loss	0.9800
19:20104236:CAGGG:C	acceptor_loss	0.9800
19:20104363:TTGG:T	donor_loss	0.9800
19:20104364:TGG:T	donor_loss	0.9800
19:20104365:GGTGA:G	donor_loss	0.9800
19:20104366:G:GC	donor_loss	0.9800
19:20104368:G:GG	donor_loss	0.9800
19:20105314:CAG:C	donor_loss	0.9800
19:20105316:GG:G	donor_loss	0.9800
19:20105317:G:A	donor_loss	0.9800
19:20105318:TAGG:T	donor_loss	0.9800

AlphaMissense

3998 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:20119106:T:C	F518L	0.989
19:20119108:C:A	F518L	0.989
19:20119108:C:G	F518L	0.989
19:20119190:T:C	F546L	0.989
19:20119192:T:A	F546L	0.989
19:20119192:T:G	F546L	0.989
19:20118938:T:C	F462L	0.985
19:20118940:C:A	F462L	0.985
19:20118940:C:G	F462L	0.985
19:20119022:T:C	F490L	0.985
19:20119024:C:A	F490L	0.985
19:20119024:C:G	F490L	0.985
19:20118770:T:C	F406L	0.983
19:20118772:C:A	F406L	0.983
19:20118772:C:G	F406L	0.983
19:20118434:T:C	F294L	0.981
19:20118436:T:A	F294L	0.981
19:20118436:T:G	F294L	0.981
19:20118686:T:C	F378L	0.981
19:20118688:T:A	F378L	0.981
19:20118688:T:G	F378L	0.981
19:20119274:T:C	F574L	0.981
19:20119276:T:A	F574L	0.981
19:20119276:T:G	F574L	0.981
19:20118602:T:C	F350L	0.980
19:20118604:C:A	F350L	0.980
19:20118604:C:G	F350L	0.980
19:20118854:T:C	F434L	0.971
19:20118856:C:A	F434L	0.971
19:20118856:C:G	F434L	0.971

dbSNP variants (sampled 300 via entrez): RS1000170067 (19:20115935 G>A), RS1000177202 (19:20091977 T>G), RS1000247839 (19:20096367 C>G), RS1000334959 (19:20087889 G>A), RS1000352346 (19:20101650 C>T), RS1000488124 (19:20101354 A>C,G), RS1000509928 (19:20106782 A>G), RS1000619304 (19:20111571 T>G), RS1000670891 (19:20079040 A>G,T), RS1000932215 (19:20089010 A>G), RS1000948790 (19:20080783 A>C), RS1001054347 (19:20106669 G>A), RS1001210583 (19:20078808 A>C,G), RS1001225939 (19:20083168 C>A), RS1001311413 (19:20116699 T>C)

Disease associations

OMIM: gene MIM:603973 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003542_169	Night sleep phenotypes	7.000000e-06
GCST008758_78	Pre-treatment viral load in HIV-1 infection	9.000000e-16
GCST90013406_93	Liver enzyme levels (alkaline phosphatase)	5.000000e-20

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010125	viral load
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	2
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
arsenite	decreases expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	increases expression	1
Acetaminophen	increases expression	1
Cadmium	increases expression	1
Methapyrilene	increases methylation	1
Tobacco Smoke Pollution	decreases expression	1
Vanadates	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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