ZNF98

Summary

ZNF98 (zinc finger protein 98, HGNC:13174) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 98 (A6NK75). 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 148198 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 103 total
• MANE Select transcript: NM_001098626

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13174
Approved symbol	ZNF98
Name	zinc finger protein 98
Location	19p12
Locus type	gene with protein product
Status	Approved
Aliases	ZNF739, F7175
Ensembl gene	ENSG00000197360
Ensembl biotype	protein_coding
OMIM	603980
Entrez	148198

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000357774, ENST00000593657, ENST00000593802, ENST00000599879, ENST00000601553

RefSeq mRNA: 1 — MANE Select: NM_001098626 NM_001098626

CCDS: CCDS46031

Canonical transcript exons

ENST00000357774 — 4 exons

Exon	Start	End
ENSE00001433568	22391019	22392981
ENSE00001549541	22422195	22422346
ENSE00002283366	22402789	22402884
ENSE00003650572	22403386	22403512

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 89.69.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1603 / max 114.8289, expressed in 204 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180253	0.6358	118
180252	0.3191	121
180251	0.2054	73

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.69	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.67	gold quality
body of pancreas	UBERON:0001150	81.31	gold quality
pancreas	UBERON:0001264	77.87	gold quality
caudate nucleus	UBERON:0001873	77.57	gold quality
quadriceps femoris	UBERON:0001377	75.83	gold quality
putamen	UBERON:0001874	75.32	gold quality
cerebellar vermis	UBERON:0004720	74.40	gold quality
testis	UBERON:0000473	73.74	gold quality
left ovary	UBERON:0002119	72.07	gold quality
left testis	UBERON:0004533	72.07	gold quality
right testis	UBERON:0004534	72.03	gold quality
ovary	UBERON:0000992	71.75	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	71.53	gold quality
islet of Langerhans	UBERON:0000006	71.50	gold quality
primary visual cortex	UBERON:0002436	71.36	gold quality
right frontal lobe	UBERON:0002810	70.67	gold quality
anterior cingulate cortex	UBERON:0009835	69.79	gold quality
superior frontal gyrus	UBERON:0002661	69.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	68.92	gold quality
right ovary	UBERON:0002118	68.44	gold quality
cerebral cortex	UBERON:0000956	68.38	gold quality
ventricular zone	UBERON:0003053	67.99	gold quality
frontal cortex	UBERON:0001870	67.97	gold quality
adrenal tissue	UBERON:0018303	66.51	gold quality
smooth muscle tissue	UBERON:0001135	66.33	gold quality
prefrontal cortex	UBERON:0000451	65.75	gold quality
nucleus accumbens	UBERON:0001882	65.19	gold quality
ganglionic eminence	UBERON:0004023	63.98	gold quality
descending thoracic aorta	UBERON:0002345	63.94	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-6819	yes	132.09
E-ANND-3	yes	7.23
E-HCAD-30	no	491.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting ZNF98, 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-3064-3P	100.00	70.09	1254
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-4645-3P	99.76	69.33	993
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-4728-3P	99.47	68.94	981
HSA-MIR-4273	99.45	67.93	1206
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-6768-3P	99.14	67.38	1319
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-34B-3P	98.70	67.40	1171
HSA-MIR-216B-3P	98.55	67.19	1223
HSA-MIR-1914-5P	97.83	66.21	807
HSA-MIR-8055	97.62	66.09	1023
HSA-MIR-500A-3P	97.60	67.48	595
HSA-MIR-6500-3P	97.42	67.20	867
HSA-MIR-3152-5P	96.98	66.88	819
HSA-MIR-4680-5P	96.43	67.15	893
HSA-MIR-4484	96.35	64.08	382

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000099025

Paralogs (18): ZNF430 (ENSG00000118620), ZNF92 (ENSG00000146757), ZNF66 (ENSG00000160229), ZNF22 (ENSG00000165512), ZNF680 (ENSG00000173041), ZNF114 (ENSG00000178150), ZFP41 (ENSG00000181638), ZNF730 (ENSG00000183850), ZNF479 (ENSG00000185177), ZNF626 (ENSG00000188171), ZNF431 (ENSG00000196705), ZNF100 (ENSG00000197020), ZNF257 (ENSG00000197134), ZNF675 (ENSG00000197372), ZNF273 (ENSG00000198039), ZNF737 (ENSG00000237440), ZNF253 (ENSG00000256771), ZNF723 (ENSG00000268696)

Protein

Protein identifiers

Zinc finger protein 98 — A6NK75 (reviewed: A6NK75)

Alternative names: Zinc finger protein 739, Zinc finger protein F7175

All UniProt accessions (4): A6NK75, M0QZH9, M0QZS3, M0R243

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_001092096* (*=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 (16 total): zinc finger region 13, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NK75-F1	72.72	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): chr19p12, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR155_5P, MIR7156_5P, MIR216B_3P, MIR4273, MIR383_3P, MIR500A_3P, MIR1914_5P, DESCARTES_MAIN_FETAL_ADRENOCORTICAL_CELLS, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), negative regulation of transcription by RNA polymerase II (GO:0000122), 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 repressor activity, RNA polymerase II-specific (GO:0001227), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

334 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF98	DTWD1	Q8N5C7	567
ZNF98	TMEM14B	Q9NUH8	471
ZNF98	SACK1F	Q8NEG4	447
ZNF98	ANKRD20A4P	Q4UJ75	447
ZNF98	ANKRD20A2P	Q5SQ80	447
ZNF98	RNF166	Q96A37	398
ZNF98	GLIPR1L2	Q4G1C9	392
ZNF98	FAM72B	Q86X60	387
ZNF98	VCF2	Q5XKR9	377
ZNF98	FAM72C	H0Y354	373
ZNF98	KRTAP9-2	Q9BYQ4	370
ZNF98	FAM72A	Q5TYM5	367
ZNF98	DHRS13	Q6UX07	366
ZNF98	FRG2C	A6NGY1	359
ZNF98	ZNG1F	Q4V339	358
ZNF98	ZNG1C	Q5JTY5	358

IntAct

0 interactions, top by confidence:

BioGRID (1): ZNF98 (Affinity Capture-MS)

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

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	89
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

656 predictions. Top by Δscore:

Variant	Effect	Δscore
19:22403425:T:A	donor_gain	1.0000
19:22392979:CAA:C	acceptor_gain	0.9900
19:22392982:C:CC	acceptor_gain	0.9900
19:22402882:TAC:T	acceptor_gain	0.9900
19:22402883:ACCTG:A	acceptor_loss	0.9900
19:22402884:CCTGT:C	acceptor_loss	0.9900
19:22402887:G:C	acceptor_loss	0.9900
19:22403378:ATCCT:A	donor_loss	0.9900
19:22403380:CCTCA:C	donor_loss	0.9900
19:22403381:CTCA:C	donor_loss	0.9900
19:22403382:TCAC:T	donor_loss	0.9900
19:22403383:C:CA	donor_loss	0.9900
19:22403384:A:AC	donor_gain	0.9900
19:22403384:A:AT	donor_loss	0.9900
19:22403384:AC:A	donor_gain	0.9900
19:22403385:C:CA	donor_loss	0.9900
19:22403385:C:CC	donor_gain	0.9900
19:22403385:CC:C	donor_gain	0.9900
19:22403385:CCCA:C	donor_gain	0.9900
19:22403509:CTCC:C	acceptor_gain	0.9900
19:22403511:CC:C	acceptor_gain	0.9900
19:22403512:CC:C	acceptor_gain	0.9900
19:22403512:CCTG:C	acceptor_loss	0.9900
19:22403513:CTGAA:C	acceptor_loss	0.9900
19:22403514:T:A	acceptor_loss	0.9900
19:22405206:A:AC	donor_gain	0.9900
19:22405207:C:CC	donor_gain	0.9900
19:22392977:TACAA:T	acceptor_gain	0.9800
19:22402784:CCTA:C	donor_loss	0.9800
19:22402786:TACC:T	donor_loss	0.9800

AlphaMissense

3803 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:22391822:A:C	F471L	0.993
19:22391822:A:T	F471L	0.993
19:22391824:A:G	F471L	0.993
19:22391906:A:C	F443L	0.993
19:22391906:A:T	F443L	0.993
19:22391908:A:G	F443L	0.993
19:22391738:A:C	F499L	0.991
19:22391738:A:T	F499L	0.991
19:22391740:A:G	F499L	0.991
19:22391654:A:C	F527L	0.984
19:22391654:A:T	F527L	0.984
19:22391656:A:G	F527L	0.984
19:22391889:A:G	L449P	0.983
19:22392494:A:C	F247L	0.981
19:22392494:A:T	F247L	0.981
19:22392496:A:G	F247L	0.981
19:22391721:A:G	L505P	0.980
19:22392326:A:C	F303L	0.976
19:22392326:A:T	F303L	0.976
19:22392328:A:G	F303L	0.976
19:22392242:A:C	F331L	0.974
19:22392242:A:T	F331L	0.974
19:22392244:A:G	F331L	0.974
19:22392410:A:C	F275L	0.973
19:22392410:A:T	F275L	0.973
19:22392412:A:G	F275L	0.973
19:22391990:A:C	F415L	0.969
19:22391990:A:T	F415L	0.969
19:22391992:A:G	F415L	0.969
19:22392158:A:C	F359L	0.969

dbSNP variants (sampled 300 via entrez): RS1000141332 (19:22390777 C>A), RS1000201478 (19:22390579 TA>T,TAA), RS1000285273 (19:22403042 T>C), RS1000311900 (19:22396648 T>C), RS1000443447 (19:22402649 T>C), RS1000619349 (19:22401656 T>C), RS1000968036 (19:22407432 G>A), RS1001108250 (19:22422600 G>A), RS1001393658 (19:22412201 A>T), RS1001422475 (19:22418108 A>G), RS1001544140 (19:22421372 T>C), RS1001696669 (19:22423483 G>A), RS1001910524 (19:22416495 T>C), RS1002057019 (19:22421639 T>C), RS1002279672 (19:22422680 T>C)

Disease associations

OMIM: gene MIM:603980 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST001408_8	Response to statins (LDL cholesterol change)	3.000000e-07
GCST001713_26	Dental caries	1.000000e-06
GCST001786_25	Dental caries	3.000000e-06
GCST004138_7	Early-onset Parkinson’s disease	6.000000e-25
GCST006186_7	Systolic blood pressure x smoking status (current vs non-current) interaction (1df test)	2.000000e-07
GCST006195_93	Systolic blood pressure x smoking status (current vs non-current) interaction (2df test)	4.000000e-08
GCST90093092_5	DHEAS levels	2.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007804	LDL cholesterol change measurement
EFO:0006335	systolic blood pressure
EFO:0006527	smoking status measurement
EFO:0007001	dehydroepiandrosterone sulphate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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