ZNF275

Summary

ZNF275 (zinc finger protein 275, HGNC:13069) is a protein-coding gene on chromosome Xq28, encoding Zinc finger protein 275 (Q9NSD4). May be involved in transcriptional regulation.

This gene encodes a zinc finger protein that appears to be conserved in eutheria. Its function has not yet been established.

Source: NCBI Gene 10838 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_001367757

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13069
Approved symbol	ZNF275
Name	zinc finger protein 275
Location	Xq28
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000063587
Ensembl biotype	protein_coding
Entrez	10838

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000370249, ENST00000370251, ENST00000438239, ENST00000647705, ENST00000650114

RefSeq mRNA: 2 — MANE Select: NM_001367757 NM_001080485, NM_001367757

CCDS: CCDS48188, CCDS94693

Canonical transcript exons

ENST00000650114 — 4 exons

Exon	Start	End
ENSE00000000175	153334153	153334285
ENSE00000869198	153345520	153345621
ENSE00001452162	153336634	153336710
ENSE00003832331	153346819	153352926

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 95.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.6714 / max 327.3902, expressed in 1747 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198031	8.3549	1728
198030	0.6431	409
198032	0.3513	153
198033	0.3221	153

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal cortex	UBERON:0001235	95.17	gold quality
right adrenal gland	UBERON:0001233	95.08	gold quality
left adrenal gland	UBERON:0001234	95.06	gold quality
left adrenal gland cortex	UBERON:0035825	94.89	gold quality
right adrenal gland cortex	UBERON:0035827	94.86	gold quality
adrenal gland	UBERON:0002369	94.73	gold quality
adrenal tissue	UBERON:0018303	93.70	gold quality
tibia	UBERON:0000979	92.72	gold quality
ileal mucosa	UBERON:0000331	92.31	gold quality
tibialis anterior	UBERON:0001385	92.15	silver quality
pancreatic ductal cell	CL:0002079	90.76	silver quality
seminal vesicle	UBERON:0000998	89.92	gold quality
visceral pleura	UBERON:0002401	89.40	gold quality
corpus epididymis	UBERON:0004359	89.13	gold quality
cartilage tissue	UBERON:0002418	88.96	gold quality
parietal pleura	UBERON:0002400	88.73	gold quality
caput epididymis	UBERON:0004358	88.70	gold quality
left ovary	UBERON:0002119	87.71	gold quality
left ventricle myocardium	UBERON:0006566	87.70	gold quality
ovary	UBERON:0000992	87.01	gold quality
cardiac muscle of right atrium	UBERON:0003379	86.83	silver quality
cauda epididymis	UBERON:0004360	86.57	gold quality
germinal epithelium of ovary	UBERON:0001304	86.45	gold quality
deltoid	UBERON:0001476	86.26	silver quality
right ovary	UBERON:0002118	86.14	gold quality
medial globus pallidus	UBERON:0002477	85.68	gold quality
adult organism	UBERON:0007023	85.40	gold quality
globus pallidus	UBERON:0001875	84.16	gold quality
postcentral gyrus	UBERON:0002581	83.96	gold quality
trabecular bone tissue	UBERON:0002483	83.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2550.1	ZNF275	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

261 targeting ZNF275, 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-656-3P	100.00	72.15	2788
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-LET-7A-5P	99.98	72.29	1790

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-207i20.2	ENSDARG00000099986

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), 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), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 275 — Q9NSD4 (reviewed: Q9NSD4)

All UniProt accessions (2): Q9NSD4, A6NFS0

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?
Q9NSD4-1	1	yes
Q9NSD4-2	2

RefSeq proteins (2): NP_001073954, NP_001354686* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096

UniProt features (19 total): zinc finger region 11, compositionally biased region 3, region of interest 2, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NSD4-F1	72.83	0.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): GCM_MAP4K4, BILD_E2F3_ONCOGENIC_SIGNATURE, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN, GCM_NF2, GCM_CALM1, OSMAN_BLADDER_CANCER_DN, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GCM_BMPR2, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, WONG_ADULT_TISSUE_STEM_MODULE, GCM_RAN, chrXq28, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIER1_TARGET_GENES

GO Biological Process (1): 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), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), 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	2
regulation of DNA-templated transcription	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
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

394 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF275	ATP1B4	Q9UN42	523
ZNF275	PIP4K2C	Q8TBX8	472
ZNF275	TEX28	O15482	400
ZNF275	RNF133	Q8WVZ7	396
ZNF275	SPTY2D1	Q68D10	393
ZNF275	MSANTD3	Q96H12	393
ZNF275	WDR44	Q5JSH3	368
ZNF275	RNASE8	Q8TDE3	366
ZNF275	PRR12	Q9ULL5	362
ZNF275	MAP7D3	Q8IWC1	350
ZNF275	SH3GL2	Q99962	349
ZNF275	PUSL1	Q8N0Z8	348
ZNF275	DNAJC5G	Q8N7S2	329
ZNF275	DRC5	Q5JU00	328
ZNF275	NHSL1	Q5SYE7	323

IntAct

38 interactions, top by confidence:

A	B	Type	Score
ZNF648	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
LIN28A	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
ZNF837	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
RBM10	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
TRAF4	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
BAHD1	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
ZNF792	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
ZNF329	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
RNF4	ZNF275	psi-mi:“MI:0915”(physical association)	0.560
CNBP	NOP56	psi-mi:“MI:0914”(association)	0.350
ZNF648	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
ZNF275	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.000
ZNF275	TRIM41	psi-mi:“MI:0915”(physical association)	0.000
LIN28A	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
ZNF837	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
RBM10	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
TRAF4	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
TRIM41	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
BAHD1	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
ZNF792	ZNF275	psi-mi:“MI:0915”(physical association)	0.000
ZNF275	RNF4	psi-mi:“MI:0915”(physical association)	0.000
ZNF275	ZNF329	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (27): ZNF275 (Affinity Capture-MS), ZNF275 (Affinity Capture-MS), ZNF275 (Affinity Capture-RNA), RNF4 (Two-hybrid), TRAF4 (Two-hybrid), LIN28A (Two-hybrid), BAHD1 (Two-hybrid), TRIM41 (Two-hybrid), ZNF837 (Two-hybrid), ZNF648 (Two-hybrid), ZNF792 (Two-hybrid), ZNF329 (Two-hybrid), RBM10 (Two-hybrid), KRTAP10-9 (Two-hybrid), ZNF275 (Affinity Capture-MS)

ESM2 similar proteins: A3KN32, A6NM28, A8K8V0, E9PYI1, O75467, O95201, P10072, P10075, P10078, P10754, P28698, P30373, P52736, Q0VCC5, Q14929, Q16587, Q17QR7, Q29RZ4, Q3KNW1, Q3TDE8, Q3US17, Q58DK7, Q5RJR4, Q5T619, Q5TEC3, Q5U4E2, Q62396, Q68H95, Q6AW86, Q6PGE4, Q6ZMY9, Q7Z398, Q7Z7K2, Q8BI73, Q8BIF9, Q8BIQ3, Q8BKK5, Q8JZL0, Q8N393, Q8R0T2

Diamond homologs: A6QR00, P0CG23, P18735, Q569E7, Q5TEC3, Q6H236, Q6ZNH5, Q8BI66, Q8NF99, Q8TF50, Q96EG3, Q9H7R5, Q9NSD4, Q7Z7K2, Q8BI67, Q8BI73, Q3US17, Q5EBL2, Q6DD87, Q8BI69, Q8BIF9, Q8BIQ3, Q8CJ78, Q8NCA9, Q8TBZ5, Q96BV0, Q96MX3, Q9H4T2, A1L2U9, B1WAZ8, B1WBU4, E9PZZ1, O14258, O75362, P39770, P39806, P78978, P80944, Q09838, Q0IH98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

397 predictions. Top by Δscore:

Variant	Effect	Δscore
X:153345519:GGC:G	acceptor_gain	1.0000
X:153345619:CTGG:C	donor_loss	1.0000
X:153344420:C:G	donor_gain	0.9900
X:153344437:A:T	donor_gain	0.9900
X:153344785:G:GT	donor_gain	0.9900
X:153345513:T:G	acceptor_gain	0.9900
X:153345518:A:AG	acceptor_gain	0.9900
X:153345519:G:GG	acceptor_gain	0.9900
X:153345610:C:G	donor_gain	0.9900
X:153345622:G:GG	donor_gain	0.9900
X:153345624:G:GC	donor_loss	0.9900
X:153346816:CAG:C	acceptor_loss	0.9900
X:153346817:A:AC	acceptor_loss	0.9900
X:153346817:A:AG	acceptor_gain	0.9900
X:153346818:G:GA	acceptor_gain	0.9900
X:153346818:G:GT	acceptor_loss	0.9900
X:153346818:GAAA:G	acceptor_gain	0.9900
X:153344775:TGTGG:T	donor_loss	0.9800
X:153344776:GTGG:G	donor_gain	0.9800
X:153344778:GG:G	donor_gain	0.9800
X:153344779:GG:G	donor_gain	0.9800
X:153344780:GT:G	donor_loss	0.9800
X:153344781:T:TC	donor_loss	0.9800
X:153345512:A:AG	acceptor_gain	0.9800
X:153345514:GAGCA:G	acceptor_loss	0.9800
X:153345609:GC:G	donor_gain	0.9800
X:153346811:C:CA	acceptor_gain	0.9800
X:153346818:GA:G	acceptor_gain	0.9800
X:153346818:GAA:G	acceptor_gain	0.9800
X:153344764:A:T	donor_gain	0.9700

AlphaMissense

2862 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:153347337:T:C	F218L	0.999
X:153347339:C:A	F218L	0.999
X:153347339:C:G	F218L	0.999
X:153347505:T:C	F274L	0.999
X:153347507:C:A	F274L	0.999
X:153347507:C:G	F274L	0.999
X:153347589:T:C	F302L	0.999
X:153347591:C:A	F302L	0.999
X:153347591:C:G	F302L	0.999
X:153347608:T:C	L308P	0.999
X:153347673:T:C	F330L	0.999
X:153347675:C:A	F330L	0.999
X:153347675:C:G	F330L	0.999
X:153347757:T:C	F358L	0.999
X:153347759:C:A	F358L	0.999
X:153347759:C:G	F358L	0.999
X:153347841:T:C	F386L	0.999
X:153347843:C:A	F386L	0.999
X:153347843:C:G	F386L	0.999
X:153347282:T:A	H199Q	0.998
X:153347282:T:G	H199Q	0.998
X:153347356:T:C	L224P	0.998
X:153347421:T:C	F246L	0.998
X:153347423:C:A	F246L	0.998
X:153347423:C:G	F246L	0.998
X:153347440:T:C	L252P	0.998
X:153347450:C:A	H255Q	0.998
X:153347450:C:G	H255Q	0.998
X:153347506:T:C	F274S	0.998
X:153347534:C:A	H283Q	0.998

dbSNP variants (sampled 300 via entrez): RS1000474864 (X:153343204 G>C), RS1000527425 (X:153343517 T>C), RS1000687346 (X:153334423 G>A), RS1000769373 (X:153351848 G>A), RS1001568772 (X:153352649 A>G), RS1001654031 (X:153344150 C>T), RS1001664123 (X:153344432 C>T), RS1001861611 (X:153334965 G>A,C), RS1002953823 (X:153339656 T>C), RS1003329620 (X:153345963 G>A), RS1003339815 (X:153346561 A>G), RS1003586492 (X:153337639 G>A), RS1003816184 (X:153335941 C>T), RS1004479348 (X:153350949 C>T), RS1004710637 (X:153343035 A>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Estradiol	increases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
sulforaphane	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
aflatoxin B2	decreases methylation	1
beta-methylcholine	affects expression	1
abrine	decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Vehicle Emissions	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Lead	decreases expression	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases methylation	1
Zinc	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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