ZNF250

Summary

ZNF250 (zinc finger protein 250, HGNC:13044) is a protein-coding gene on chromosome 8q24.3, encoding Zinc finger protein 250 (P15622). May be involved in transcriptional regulation.

Enables identical protein binding activity and 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 58500 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_001109689

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13044
Approved symbol	ZNF250
Name	zinc finger protein 250
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC9718, ZFP647
Ensembl gene	ENSG00000196150
Ensembl biotype	protein_coding
Entrez	58500

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 28 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron

ENST00000292579, ENST00000417550, ENST00000525694, ENST00000527049, ENST00000528028, ENST00000528258, ENST00000529780, ENST00000533221, ENST00000533543, ENST00000533622, ENST00000862359, ENST00000862360, ENST00000862361, ENST00000862363, ENST00000862364, ENST00000862366, ENST00000862368, ENST00000862369, ENST00000862371, ENST00000862373, ENST00000940315, ENST00000940316, ENST00000940317, ENST00000940318, ENST00000940319, ENST00000940320, ENST00000940321, ENST00000940322, ENST00000956450, ENST00000956451, ENST00000956452, ENST00000956453

RefSeq mRNA: 12 — MANE Select: NM_001109689 NM_001109689, NM_001363098, NM_001363099, NM_001363100, NM_001363101, NM_001363102, NM_001363103, NM_001363104, NM_001363105, NM_001363106, NM_001363107, NM_021061

CCDS: CCDS34972, CCDS55282

Canonical transcript exons

ENST00000417550 — 6 exons

Exon	Start	End
ENSE00001055890	144889581	144889694
ENSE00001087463	144886840	144886902
ENSE00002141412	144901399	144901453
ENSE00002151370	144876955	144882836
ENSE00002410294	144889933	144890059
ENSE00003691376	144890308	144890403

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 89.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.0977 / max 162.8225, expressed in 1733 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
95729	10.8504	1729
205404	0.1481	55
95728	0.0992	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	89.74	gold quality
ganglionic eminence	UBERON:0004023	87.57	gold quality
ventricular zone	UBERON:0003053	84.58	gold quality
skin of leg	UBERON:0001511	83.00	gold quality
popliteal artery	UBERON:0002250	81.91	gold quality
tibial artery	UBERON:0007610	81.89	gold quality
left lobe of thyroid gland	UBERON:0001120	81.74	gold quality
skin of abdomen	UBERON:0001416	81.41	gold quality
right lobe of thyroid gland	UBERON:0001119	81.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.12	gold quality
artery	UBERON:0001637	80.84	gold quality
endocervix	UBERON:0000458	80.81	gold quality
thyroid gland	UBERON:0002046	80.80	gold quality
ectocervix	UBERON:0012249	80.75	gold quality
lower esophagus mucosa	UBERON:0035834	80.54	gold quality
left ovary	UBERON:0002119	80.31	gold quality
aorta	UBERON:0000947	80.27	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.69	gold quality
right ovary	UBERON:0002118	79.48	gold quality
cerebellar hemisphere	UBERON:0002245	79.48	gold quality
apex of heart	UBERON:0002098	79.40	gold quality
body of uterus	UBERON:0009853	79.36	gold quality
cerebellar cortex	UBERON:0002129	79.32	gold quality
right hemisphere of cerebellum	UBERON:0014890	79.28	gold quality
endothelial cell	CL:0000115	79.04	silver quality
zone of skin	UBERON:0000014	79.01	gold quality
ascending aorta	UBERON:0001496	78.63	gold quality
thoracic aorta	UBERON:0001515	78.54	gold quality
right lung	UBERON:0002167	78.27	gold quality
descending thoracic aorta	UBERON:0002345	78.25	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.02

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
COL11A2
RPE65
TRIM28

JASPAR motifs

Motif	Name	Family
MA2462.1	ZNF250	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

186 targeting ZNF250, 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-4692	100.00	67.32	2066
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-3658	99.96	73.87	4379

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp647	ENSMUSG00000054967
rattus_norvegicus	Zfp647	ENSRNOG00000068661

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 250 — P15622 (reviewed: P15622)

Alternative names: Zinc finger protein 647

All UniProt accessions (8): P15622, E9PJU7, E9PKP2, E9PL28, E9PPG5, E9PQX5, F6RA56, Q3B7J8

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 (3)

UniProt ID	Names	Canonical?
P15622-1	1	yes
P15622-2	2
P15622-3	3

RefSeq proteins (12): NP_001103159, NP_001350027, NP_001350028, NP_001350029, NP_001350030, NP_001350031, NP_001350032, NP_001350033, NP_001350034, NP_001350035, NP_001350036, NP_066405 (=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 (25 total): zinc finger region 13, cross-link 6, splice variant 2, sequence conflict 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P15622-F1	75.47	0.50

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 (6): 125, 136, 148, 162, 225, 421

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 100 (showing top): HALMOS_CEBPA_TARGETS_UP, PUJANA_CHEK2_PCC_NETWORK, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, chr8q24, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, E2F2_TARGET_GENES, HHEX_TARGET_GENES, HOXB6_TARGET_GENES, NR1I2_TARGET_GENES

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

GO Molecular Function (8): 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), identical protein binding (GO:0042802), 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
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
protein 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

882 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF250	KAT14	Q9H8E8	500
ZNF250	RPS7	P23821	443
ZNF250	C8orf33	Q9H7E9	427
ZNF250	POP1	Q99575	392
ZNF250	GPATCH4	Q5T3I0	375
ZNF250	LYSMD1	Q96S90	374
ZNF250	FAM98B	Q52LJ0	372
ZNF250	OR2T8	A6NH00	370
ZNF250	TIGD5	Q53EQ6	370
ZNF250	ZHX1-C8orf76	Q96EF9	370
ZNF250	C8orf76	Q96K31	369
ZNF250	COMMD5	Q9GZQ3	369
ZNF250	XRCC3	O43542	368
ZNF250	C5orf22	Q49AR2	366
ZNF250	MROH1	Q8NDA8	361

IntAct

27 interactions, top by confidence:

A	B	Type	Score
ZNF250	LDOC1	psi-mi:“MI:0915”(physical association)	0.550
rep	ZNF250	psi-mi:“MI:0914”(association)	0.550
ZNF250	rep	psi-mi:“MI:0915”(physical association)	0.550
LDOC1	ZNF250	psi-mi:“MI:0915”(physical association)	0.550
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
Trim28	FTH1	psi-mi:“MI:0915”(physical association)	0.400
ZNF250	DBP	psi-mi:“MI:0915”(physical association)	0.370
ZNF250		psi-mi:“MI:0915”(physical association)	0.370
TNNT1	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
CCDC85B	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
ZNF250	DPPA2	psi-mi:“MI:0915”(physical association)	0.370
ZNF250	KRTAP4-12	psi-mi:“MI:0915”(physical association)	0.370
GOLGA2	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
BEGAIN	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
HOOK1	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
HOOK2	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
ZNF250	CEP44	psi-mi:“MI:0915”(physical association)	0.370
NINL	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
DVL2	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
TRIM23	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
ZNF250	ZBTB8A	psi-mi:“MI:0915”(physical association)	0.370
ZNF165	ZNF250	psi-mi:“MI:0915”(physical association)	0.370
ZNF250	SPINT1	psi-mi:“MI:0914”(association)	0.350
FMR1	ZNF250	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (164): ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid), ZNF250 (Two-hybrid)

ESM2 similar proteins: A3KN32, A3KN36, O14709, O43296, O75123, P15622, P16373, P17023, P17031, P17097, P52736, P85977, Q07230, Q12901, Q14929, Q29RZ4, Q4V8A8, Q571J5, Q5CZA5, Q5JNZ3, Q5R7I8, Q5RBX0, Q5RBY9, Q5RCD9, Q5RCX4, Q61751, Q61967, Q6GQR8, Q6IV72, Q6NX45, Q6PK81, Q6ZMS4, Q7TNU6, Q7TSH9, Q7Z398, Q7Z7L9, Q8BI99, Q8BIQ3, Q8BLB0, Q8IZ26

Diamond homologs: A2A761, A2VDP4, A3KN32, A6QLU5, A6QPT6, A7MBI1, A8MT65, B4DU55, E9PYI1, O60765, O95780, P15622, P17014, P17032, P17098, P21506, P51508, P51814, P52736, P52738, P52742, Q02975, Q06730, Q06732, Q0VCB0, Q14587, Q16587, Q2KI58, Q2M3W8, Q3V080, Q49AA0, Q4R6C2, Q4V8A8, Q571J5, Q5HYK9, Q5JUW0, Q5JVG2, Q5MCW4, Q5MYW4, Q5R4K8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1034 predictions. Top by Δscore:

Variant	Effect	Δscore
8:144889694:CCTGC:C	acceptor_loss	1.0000
8:144889695:C:A	acceptor_loss	1.0000
8:144889700:C:CT	acceptor_gain	1.0000
8:144889701:G:C	acceptor_gain	1.0000
8:144889701:G:GC	acceptor_gain	1.0000
8:144889931:AC:A	donor_gain	1.0000
8:144889932:CC:C	donor_gain	1.0000
8:144890302:GCTTA:G	donor_loss	1.0000
8:144890303:CTTA:C	donor_loss	1.0000
8:144890304:TTA:T	donor_loss	1.0000
8:144890305:TA:T	donor_loss	1.0000
8:144890306:ACCTG:A	donor_loss	1.0000
8:144890401:GGG:G	acceptor_gain	1.0000
8:144890402:GG:G	acceptor_gain	1.0000
8:144890404:C:CC	acceptor_gain	1.0000
8:144886903:C:CC	acceptor_gain	0.9900
8:144889577:TCA:T	donor_loss	0.9900
8:144889578:CACC:C	donor_loss	0.9900
8:144889580:C:CT	donor_loss	0.9900
8:144889691:AGTC:A	acceptor_gain	0.9900
8:144889692:GTC:G	acceptor_gain	0.9900
8:144889693:TC:T	acceptor_gain	0.9900
8:144889694:CC:C	acceptor_gain	0.9900
8:144889695:C:CC	acceptor_gain	0.9900
8:144889696:T:C	acceptor_loss	0.9900
8:144889926:GGCTT:G	donor_loss	0.9900
8:144889927:GCTT:G	donor_loss	0.9900
8:144889928:CTT:C	donor_loss	0.9900
8:144889929:TTACC:T	donor_loss	0.9900
8:144889930:T:TG	donor_loss	0.9900

AlphaMissense

3694 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:144882322:G:C	F292L	1.000
8:144882322:G:T	F292L	1.000
8:144882324:A:G	F292L	1.000
8:144882406:A:C	F264L	1.000
8:144882406:A:T	F264L	1.000
8:144882408:A:G	F264L	1.000
8:144882490:G:C	F236L	1.000
8:144882490:G:T	F236L	1.000
8:144882492:A:G	F236L	1.000
8:144881566:G:C	F544L	0.999
8:144881566:G:T	F544L	0.999
8:144881568:A:G	F544L	0.999
8:144881618:C:G	R527P	0.999
8:144881650:G:C	F516L	0.999
8:144881650:G:T	F516L	0.999
8:144881652:A:G	F516L	0.999
8:144881734:G:C	F488L	0.999
8:144881734:G:T	F488L	0.999
8:144881736:A:G	F488L	0.999
8:144882070:G:C	F376L	0.999
8:144882070:G:T	F376L	0.999
8:144882072:A:G	F376L	0.999
8:144882154:G:C	F348L	0.999
8:144882154:G:T	F348L	0.999
8:144882156:A:G	F348L	0.999
8:144882238:G:C	F320L	0.999
8:144882238:G:T	F320L	0.999
8:144882240:A:G	F320L	0.999
8:144882290:C:G	R303P	0.999
8:144882295:G:C	H301Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000031593 (8:144880272 T>A), RS1000076720 (8:144899331 A>G), RS1000110741 (8:144876664 T>C), RS1000346632 (8:144886795 C>A), RS1000518875 (8:144901123 C>T), RS1000729918 (8:144895459 G>A,T), RS1000768747 (8:144888546 G>A), RS1000890839 (8:144881952 T>G), RS1001138718 (8:144898233 T>C,G), RS1001244601 (8:144897508 T>A), RS1001359197 (8:144897711 G>A,T), RS1001381514 (8:144885456 A>G), RS1001427662 (8:144891436 G>A), RS1001585725 (8:144898944 A>G), RS1001628483 (8:144903571 C>T)

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

2 associations (top):

Study	Trait	p-value
GCST007005_3	Logical memory (immediate recall) in normal cognition	5.000000e-07
GCST007005_4	Logical memory (immediate recall) in normal cognition	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Atrazine	decreases expression	1
Benzene	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Caffeine	increases phosphorylation	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression	1
Lactic Acid	increases expression	1

Clinical trials (associated diseases)

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