ZNF75D

Summary

ZNF75D (zinc finger protein 75D, HGNC:13145) is a protein-coding gene on chromosome Xq26.3, encoding Zinc finger protein 75D (P51815). May be involved in transcriptional regulation.

This gene encodes a protein that likely functions as a transcription factor. The protein, which belongs to the ZNF75 family, includes an N-terminal SCAN domain, a KRAB box, and five C2H2-type zinc finger motifs. Another functional gene belonging to this family is located on chromosome 16, while pseudogenes have been identified on chromosomes 11 and 12. Alternative splicing results in multiple transcripts variants.

Source: NCBI Gene 7626 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 114 total
• MANE Select transcript: NM_007131

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13145
Approved symbol	ZNF75D
Name	zinc finger protein 75D
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	ZKSCAN24, D8C6, ZSCAN28
Ensembl gene	ENSG00000186376
Ensembl biotype	protein_coding
OMIM	314997
Entrez	7626

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000370764, ENST00000370766, ENST00000469456, ENST00000494295, ENST00000865785, ENST00000865786, ENST00000865787, ENST00000865788, ENST00000865789, ENST00000865790, ENST00000865791, ENST00000942296, ENST00000942297, ENST00000942298

RefSeq mRNA: 2 — MANE Select: NM_007131 NM_001185063, NM_007131

CCDS: CCDS14648, CCDS55503

Canonical transcript exons

ENST00000370766 — 7 exons

Exon	Start	End
ENSE00001257659	135292281	135292473
ENSE00001257694	135295768	135296039
ENSE00001257730	135291472	135291563
ENSE00001257745	135285791	135287846
ENSE00001453586	135293730	135294258
ENSE00001635051	135291009	135291135
ENSE00001889449	135341768	135344109

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 86.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2668 / max 60.9877, expressed in 1626 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200619	3.6226	1469
200620	1.4706	869
200618	0.1736	91

Top tissues by expression

274 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	86.97	gold quality
right adrenal gland cortex	UBERON:0035827	86.60	gold quality
right adrenal gland	UBERON:0001233	86.29	gold quality
left adrenal gland	UBERON:0001234	84.79	gold quality
left adrenal gland cortex	UBERON:0035825	84.79	gold quality
adrenal cortex	UBERON:0001235	84.54	gold quality
adrenal tissue	UBERON:0018303	83.96	gold quality
adrenal gland	UBERON:0002369	83.85	gold quality
buccal mucosa cell	CL:0002336	82.82	silver quality
body of pancreas	UBERON:0001150	82.54	gold quality
spleen	UBERON:0002106	82.42	gold quality
granulocyte	CL:0000094	82.03	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.74	gold quality
right lobe of liver	UBERON:0001114	81.47	gold quality
right uterine tube	UBERON:0001302	81.24	gold quality
left lobe of thyroid gland	UBERON:0001120	80.91	gold quality
metanephros cortex	UBERON:0010533	80.65	gold quality
right lobe of thyroid gland	UBERON:0001119	80.50	gold quality
thyroid gland	UBERON:0002046	80.30	gold quality
prostate gland	UBERON:0002367	79.77	gold quality
small intestine Peyer’s patch	UBERON:0003454	79.40	gold quality
right lung	UBERON:0002167	79.33	gold quality
endometrium epithelium	UBERON:0004811	79.32	gold quality
body of stomach	UBERON:0001161	79.29	gold quality
right ovary	UBERON:0002118	79.12	gold quality
ventricular zone	UBERON:0003053	78.85	gold quality
monocyte	CL:0000576	78.84	gold quality
leukocyte	CL:0000738	78.76	gold quality
transverse colon	UBERON:0001157	78.71	gold quality
pancreas	UBERON:0001264	78.67	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6386	no	526.52
E-ANND-3	no	4.81

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1601.1	ZNF75D	More than 3 adjacent zinc fingers
MA1601.2	ZNF75D	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28473536

miRNA regulators (miRDB)

55 targeting ZNF75D, 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-340-5P	100.00	72.50	4437
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-577	99.78	69.13	2479
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-4728-3P	99.47	68.94	981
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-296-3P	99.21	66.56	474
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582

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), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), 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 75D — P51815 (reviewed: P51815)

Alternative names: Zinc finger protein 75, Zinc finger protein 82

All UniProt accessions (1): P51815

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.

Isoforms (2)

UniProt ID	Names	Canonical?
P51815-1	1	yes
P51815-2	2

RefSeq proteins (2): NP_001171992, NP_009062* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily

Pfam: PF00096, PF01352, PF02023

UniProt features (14 total): zinc finger region 5, domain 2, compositionally biased region 2, region of interest 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P51815-F1	63.21	0.08

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 60 (showing top): BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP, MODULE_285, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, BLALOCK_ALZHEIMERS_DISEASE_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LIU_PROSTATE_CANCER_DN, chrXq26, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, RBM34_TARGET_GENES, SFMBT1_TARGET_GENES, ZNF407_TARGET_GENES, ZNF423_TARGET_GENES, MIR153_5P, MIR1250_3P, MIR4652_3P

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

900 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF75D	ZNF274	Q96GC6	585
ZNF75D	PAPLN	O95428	478
ZNF75D	DNAJC16	Q9Y2G8	474
ZNF75D	CCDC59	Q9P031	459
ZNF75D	ELP4	Q96EB1	449
ZNF75D	NEK8	Q86SG6	397
ZNF75D	SC5D	O75845	380
ZNF75D	MAGEH1	Q9H213	376
ZNF75D	NHLH2	Q02577	372
ZNF75D	NEK9	Q8TD19	370
ZNF75D	ATP10A	O60312	366
ZNF75D	PURA	Q00577	351
ZNF75D	PCSK1	P29120	349
ZNF75D	CCDC85B	Q15834	346
ZNF75D	ZC3H6	P61129	333

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ZNF75D	MRPS14	psi-mi:“MI:0914”(association)	0.350
sthA	ZNF75D	psi-mi:“MI:0915”(physical association)	0.000
	ZNF75D	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): ZNF75D (Affinity Capture-MS), ZNF75D (Affinity Capture-RNA)

ESM2 similar proteins: A1YEQ3, A1YEV9, A1YFW6, A1YG26, A1YG48, A1YG60, A2T6W2, A2T712, A2T736, A2T7L7, A6QNZ0, O14978, O15535, O95125, P17022, P17029, P49910, P51815, P59923, Q07231, Q15776, Q16670, Q1LZ87, Q3MJ62, Q3URR7, Q4KLI1, Q4R8H9, Q53GI3, Q5R670, Q5R741, Q5RJ54, Q63HK3, Q642B9, Q6P9G9, Q810A1, Q86W11, Q8BGS3, Q8CF60, Q8NF99, Q92670

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	8
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1237 predictions. Top by Δscore:

Variant	Effect	Δscore
X:135291005:TTACC:T	donor_loss	1.0000
X:135291006:TA:T	donor_loss	1.0000
X:135291007:A:C	donor_loss	1.0000
X:135291008:C:CA	donor_loss	1.0000
X:135291131:AAACT:A	acceptor_gain	1.0000
X:135291132:AACT:A	acceptor_gain	1.0000
X:135291134:CT:C	acceptor_gain	1.0000
X:135291136:C:CC	acceptor_gain	1.0000
X:135292275:CCTCA:C	donor_loss	1.0000
X:135292276:CTCA:C	donor_loss	1.0000
X:135292277:TCA:T	donor_loss	1.0000
X:135292278:CACCT:C	donor_loss	1.0000
X:135292279:A:T	donor_loss	1.0000
X:135343323:CAG:C	donor_gain	1.0000
X:135291041:A:AC	donor_gain	0.9900
X:135291133:ACTCT:A	acceptor_gain	0.9900
X:135291135:TC:T	acceptor_loss	0.9900
X:135291136:CTAAA:C	acceptor_loss	0.9900
X:135291137:T:A	acceptor_loss	0.9900
X:135291561:CAG:C	acceptor_gain	0.9900
X:135292280:CCT:C	donor_gain	0.9900
X:135292474:CTAG:C	acceptor_loss	0.9900
X:135294257:CA:C	acceptor_gain	0.9900
X:135294259:C:CC	acceptor_gain	0.9900
X:135343308:A:AC	donor_gain	0.9900
X:135343309:C:CC	donor_gain	0.9900
X:135291034:AT:A	donor_gain	0.9800
X:135291134:CTCT:C	acceptor_gain	0.9800
X:135292472:ACCT:A	acceptor_gain	0.9800
X:135292473:CCT:C	acceptor_gain	0.9800

AlphaMissense

3410 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:135287296:G:C	F458L	1.000
X:135287296:G:T	F458L	1.000
X:135287298:A:G	F458L	1.000
X:135287380:A:C	F430L	1.000
X:135287380:A:T	F430L	1.000
X:135287382:A:G	F430L	1.000
X:135287279:A:G	L464P	0.999
X:135287297:A:G	F458S	0.999
X:135287341:G:C	H443Q	0.999
X:135287341:G:T	H443Q	0.999
X:135287464:A:C	F402L	0.999
X:135287464:A:T	F402L	0.999
X:135287466:A:G	F402L	0.999
X:135287548:G:C	F374L	0.999
X:135287548:G:T	F374L	0.999
X:135287550:A:G	F374L	0.999
X:135287212:A:C	F486L	0.998
X:135287212:A:T	F486L	0.998
X:135287214:A:G	F486L	0.998
X:135287269:G:C	H467Q	0.998
X:135287269:G:T	H467Q	0.998
X:135287343:G:C	H443D	0.998
X:135287353:G:C	H439Q	0.998
X:135287353:G:T	H439Q	0.998
X:135287363:A:G	L436P	0.998
X:135287381:A:G	F430S	0.998
X:135287267:T:G	Q468P	0.997
X:135287271:G:C	H467D	0.997
X:135287323:A:C	F449L	0.997
X:135287323:A:T	F449L	0.997

dbSNP variants (sampled 300 via entrez): RS1000015206 (X:135285173 G>A), RS1000123787 (X:135275937 C>A), RS1000125013 (X:135345515 G>A), RS1000236163 (X:135284526 T>G), RS1000308748 (X:135276671 G>A), RS1000572361 (X:135298856 G>T), RS1000641570 (X:135319087 C>A,T), RS1000680841 (X:135259824 C>T), RS1000701019 (X:135328728 C>A), RS1000739274 (X:135338448 C>T), RS1000909324 (X:135278485 C>G,T), RS1000913397 (X:135268028 G>T), RS1000933549 (X:135318803 T>C), RS1000963877 (X:135267522 G>T), RS1001011522 (X:135289647 C>G)

Disease associations

OMIM: gene MIM:314997 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects expression, affects methylation, decreases expression, increases methylation	4
Aflatoxin B1	decreases methylation, increases methylation	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
geraniol	increases expression	1
methylselenic acid	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Doxorubicin	decreases expression	1
Phthalic Acids	decreases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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