ZNF75A

Summary

ZNF75A (zinc finger protein 75A, HGNC:13146) is a protein-coding gene on chromosome 16p13.3, encoding Zinc finger protein 75A (Q96N20). May be involved in transcriptional regulation.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 7627 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001302109

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13146
Approved symbol	ZNF75A
Name	zinc finger protein 75A
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31529
Ensembl gene	ENSG00000162086
Ensembl biotype	protein_coding
OMIM	601473
Entrez	7627

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 10 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000498240, ENST00000571101, ENST00000572999, ENST00000573828, ENST00000574298, ENST00000575234, ENST00000575253, ENST00000575812, ENST00000612186, ENST00000617839, ENST00000669516, ENST00000903407, ENST00000903408, ENST00000903409, ENST00000938989, ENST00000938990, ENST00000941569

RefSeq mRNA: 7 — MANE Select: NM_001302109 NM_001302109, NM_001324041, NM_001324085, NM_001352495, NM_001352497, NM_001352498, NM_153028

CCDS: CCDS10501, CCDS92095

Canonical transcript exons

ENST00000669516 — 7 exons

Exon	Start	End
ENSE00001817586	3308313	3308836
ENSE00003643326	3316912	3317022
ENSE00003854209	3313049	3313175
ENSE00003864997	3317190	3318851
ENSE00003869060	3311753	3311948
ENSE00003877833	3312677	3312768
ENSE00003899913	3305497	3305643

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 97.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.7596 / max 125.5259, expressed in 1754 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152420	14.7596	1754

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	97.09	gold quality
kidney epithelium	UBERON:0004819	95.01	silver quality
upper arm skin	UBERON:0004263	93.33	silver quality
left ventricle myocardium	UBERON:0006566	92.48	silver quality
cardia of stomach	UBERON:0001162	92.18	gold quality
buccal mucosa cell	CL:0002336	92.13	gold quality
right lobe of thyroid gland	UBERON:0001119	91.64	gold quality
ganglionic eminence	UBERON:0004023	91.53	gold quality
fallopian tube	UBERON:0003889	91.29	gold quality
left lobe of thyroid gland	UBERON:0001120	91.28	gold quality
thyroid gland	UBERON:0002046	91.20	gold quality
renal medulla	UBERON:0000362	91.07	gold quality
nipple	UBERON:0002030	90.75	gold quality
corpus callosum	UBERON:0002336	90.71	gold quality
cerebellar hemisphere	UBERON:0002245	90.46	gold quality
cerebellar cortex	UBERON:0002129	90.45	gold quality
ventricular zone	UBERON:0003053	90.44	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.36	gold quality
lymph node	UBERON:0000029	90.35	gold quality
cortical plate	UBERON:0005343	90.33	gold quality
cerebellum	UBERON:0002037	90.23	gold quality
calcaneal tendon	UBERON:0003701	90.07	gold quality
pylorus	UBERON:0001166	90.03	gold quality
inferior vagus X ganglion	UBERON:0005363	90.02	gold quality
myocardium	UBERON:0002349	90.00	silver quality
ventral tegmental area	UBERON:0002691	89.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.90	gold quality
metanephros cortex	UBERON:0010533	89.89	gold quality
sural nerve	UBERON:0015488	89.74	gold quality
pituitary gland	UBERON:0000007	89.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.36
E-CURD-135	no	833.23

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2097.1	ZNF75A	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:29638227

miRNA regulators (miRDB)

31 targeting ZNF75A, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-8070	99.07	69.30	1303
HSA-MIR-4764-5P	98.88	65.53	894
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-3938	98.72	66.07	834
HSA-MIR-124-5P	98.11	67.65	1095
HSA-MIR-219B-5P	97.91	65.80	531
HSA-MIR-3672	94.46	65.67	646

Cross-species orthologs

0 orthologs

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZKSCAN3 (ENSG00000189298), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger protein 75A — Q96N20 (reviewed: Q96N20)

All UniProt accessions (4): A0A590UJ20, A0A590UJE0, Q96N20, Q86V93

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 (7): NP_001289038, NP_001310970, NP_001311014, NP_001339424, NP_001339426, NP_001339427, NP_694573 (=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352

UniProt features (9 total): zinc finger region 5, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96N20-F1	74.43	0.45

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 45 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BAHD1_TARGET_GENES, PTPRA_TARGET_GENES, SNAPC4_TARGET_GENES, ZNF610_TARGET_GENES, MIR4698, MIR4495, MIR302E, MIR3692_3P, MIR302A_3P_MIR302B_3P_MIR302C_3P_MIR302D_3P, MIR520A_3P, MIR372_3P, MIR520D_3P

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

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), 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-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

356 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF75A	TIGD7	Q6NT04	606
ZNF75A	C14orf180	Q8N912	556
ZNF75A	OR1F1	O43749	418
ZNF75A	ZNF395	Q9H8N7	406
ZNF75A	GARIN3	Q8TC56	400
ZNF75A	CTTNBP2NL	Q9P2B4	383
ZNF75A	FLRT2	O43155	371
ZNF75A	ZNF654	Q8IZM8	354
ZNF75A	NTNG1	Q9Y2I2	339
ZNF75A	LHX4	Q969G2	329
ZNF75A	NKAPL	Q5M9Q1	313
ZNF75A	PTRH2	Q9Y3E5	310
ZNF75A	ABCA12	Q86UK0	307
ZNF75A	NICN1	Q9BSH3	306
ZNF75A	SP140L	Q9H930	304
ZNF75A	CHURC1	Q8WUH1	304

IntAct

7 interactions, top by confidence:

A	B	Type	Score
SPANXN2	ZNF75A	psi-mi:“MI:0915”(physical association)	0.560
ZNF71	NVL	psi-mi:“MI:0914”(association)	0.530
ZNF75A	TPP2	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): ZNF75A (Affinity Capture-MS), SPANXN2 (Two-hybrid), HDAC6 (Affinity Capture-MS), TPP2 (Affinity Capture-MS), C1QTNF1 (Affinity Capture-MS), ZNF75A (Affinity Capture-MS), FOCAD (Affinity Capture-MS), PACSIN2 (Affinity Capture-MS), ZNF75A (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A2A761, A2T7D2, A3KN32, A3KN36, A7MBI1, B2RXC5, E9PYI1, O43296, P0CG31, P10072, P10078, P17023, P17097, P18725, P18728, P52738, Q02525, Q07231, Q0VCB0, Q12901, Q14592, Q49AA0, Q4V8A8, Q571J5, Q5CZA5, Q5JNZ3, Q5R7I8, Q5RB33, Q5RBX0, Q5RBY9, Q61967, Q62396, Q6PF04, Q6ZNG0, Q6ZS27, Q7Z398, Q80YP6, Q8BIQ3, Q8IZ26, Q96N20

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1601 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3311944:GAGGG:G	donor_gain	1.0000
16:3312672:CACA:C	acceptor_loss	1.0000
16:3312674:CAGCT:C	acceptor_loss	1.0000
16:3312675:A:AG	acceptor_gain	1.0000
16:3312675:AGCTG:A	acceptor_loss	1.0000
16:3312676:G:GA	acceptor_gain	1.0000
16:3312676:GCT:G	acceptor_gain	1.0000
16:3312764:CCCAG:C	donor_loss	1.0000
16:3312768:GGTG:G	donor_loss	1.0000
16:3312769:G:A	donor_loss	1.0000
16:3312770:T:G	donor_loss	1.0000
16:3313047:A:AG	acceptor_gain	1.0000
16:3313048:G:GG	acceptor_gain	1.0000
16:3313048:GA:G	acceptor_gain	1.0000
16:3305481:T:TA	donor_gain	0.9900
16:3305626:G:GT	donor_gain	0.9900
16:3305709:G:GT	donor_gain	0.9900
16:3305710:G:T	donor_gain	0.9900
16:3306057:G:GT	donor_gain	0.9900
16:3308311:A:AG	acceptor_gain	0.9900
16:3308312:G:GG	acceptor_gain	0.9900
16:3311748:TCTA:T	acceptor_loss	0.9900
16:3311751:A:AC	acceptor_loss	0.9900
16:3311911:G:GT	donor_gain	0.9900
16:3311946:GGG:G	donor_gain	0.9900
16:3311947:GG:G	donor_gain	0.9900
16:3311947:GGG:G	donor_gain	0.9900
16:3311948:GG:G	donor_gain	0.9900
16:3312674:C:G	acceptor_gain	0.9900
16:3312675:AGCT:A	acceptor_gain	0.9900

AlphaMissense

3575 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3317570:T:C	F198L	0.999
16:3317572:T:A	F198L	0.999
16:3317572:T:G	F198L	0.999
16:3317654:T:C	F226L	0.999
16:3317656:C:A	F226L	0.999
16:3317656:C:G	F226L	0.999
16:3317738:T:C	F254L	0.999
16:3317740:C:A	F254L	0.999
16:3317740:C:G	F254L	0.999
16:3317695:T:A	H239Q	0.998
16:3317695:T:G	H239Q	0.998
16:3317589:T:C	L204P	0.997
16:3317711:T:C	F245L	0.997
16:3317713:C:A	F245L	0.997
16:3317713:C:G	F245L	0.997
16:3317757:T:C	L260P	0.997
16:3317683:C:A	H235Q	0.996
16:3317683:C:G	H235Q	0.996
16:3317486:T:C	F170L	0.995
16:3317488:C:A	F170L	0.995
16:3317488:C:G	F170L	0.995
16:3317571:T:C	F198S	0.995
16:3317655:T:C	F226S	0.995
16:3317681:C:G	H235D	0.995
16:3317767:C:A	H263Q	0.995
16:3317767:C:G	H263Q	0.995
16:3317779:C:A	H267Q	0.995
16:3317779:C:G	H267Q	0.995
16:3317822:T:C	F282L	0.995
16:3317824:C:A	F282L	0.995

dbSNP variants (sampled 300 via entrez): RS1000239965 (16:3317432 A>G), RS1000286048 (16:3308477 A>C,G), RS1000289238 (16:3303924 C>G), RS1000295054 (16:3312568 G>A), RS1000734700 (16:3322157 T>A,C), RS1000842669 (16:3317841 T>G), RS1000907183 (16:3317718 G>A,T), RS1001000870 (16:3312771 G>A), RS1001048991 (16:3305394 G>A,T), RS1001143115 (16:3305180 C>T), RS1001176199 (16:3312269 G>C), RS1001207295 (16:3312508 C>T), RS1001281880 (16:3304413 C>G), RS1001386352 (16:3309414 C>A,T), RS1001526640 (16:3321795 G>A)

Disease associations

OMIM: gene MIM:601473 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004735_12	Epstein-Barr virus copy number in lymphoblastoid cell lines	2.000000e-07
GCST006979_1054	Heel bone mineral density	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Valproic Acid	affects expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
ferrous chloride	decreases expression	1
aflatoxin B2	decreases methylation	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
(+)-JQ1 compound	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, affects expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1
Zinc	affects cotreatment, increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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