ZNF487

Summary

ZNF487 (zinc finger protein 487, HGNC:23488) is a protein-coding gene on chromosome 10q11.21, encoding Zinc finger protein 487 (B1APH4). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus.

Source: NCBI Gene 642819 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• MANE Select transcript: NM_001355444

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23488
Approved symbol	ZNF487
Name	zinc finger protein 487
Location	10q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000243660
Ensembl biotype	protein_coding
Entrez	642819

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 19 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000315429, ENST00000437590, ENST00000451167, ENST00000456416, ENST00000490208, ENST00000596267, ENST00000652684, ENST00000689627, ENST00000887192, ENST00000887193, ENST00000887194, ENST00000887195, ENST00000887196, ENST00000887197, ENST00000887198, ENST00000887199, ENST00000887200, ENST00000941780, ENST00000941781, ENST00000941782, ENST00000941783

RefSeq mRNA: 7 — MANE Select: NM_001355444 NM_001355444, NM_001355445, NM_001355446, NM_001355447, NM_001355448, NM_001355449, NM_001355450

CCDS: CCDS86084

Canonical transcript exons

ENST00000437590 — 4 exons

Exon	Start	End
ENSE00001463537	43481429	43483181
ENSE00002514680	43476107	43476202
ENSE00003487507	43475721	43475847
ENSE00003924620	43437111	43437262

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 94.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.8897 / max 59.4992, expressed in 1215 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
104756	1.8637	790
104757	1.0260	531

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	94.45	gold quality
bronchus	UBERON:0002185	93.45	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.45	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.79	gold quality
right uterine tube	UBERON:0001302	87.80	gold quality
left testis	UBERON:0004533	87.42	gold quality
right testis	UBERON:0004534	87.40	gold quality
oviduct epithelium	UBERON:0004804	85.98	gold quality
testis	UBERON:0000473	85.51	gold quality
epithelium of nasopharynx	UBERON:0001951	82.48	gold quality
nasopharynx	UBERON:0001728	82.47	gold quality
corpus epididymis	UBERON:0004359	82.16	gold quality
oocyte	CL:0000023	82.12	gold quality
sperm	CL:0000019	81.50	gold quality
caput epididymis	UBERON:0004358	81.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.06	gold quality
fallopian tube	UBERON:0003889	81.04	gold quality
nasal cavity mucosa	UBERON:0001826	80.92	gold quality
monocyte	CL:0000576	80.81	gold quality
leukocyte	CL:0000738	80.48	gold quality
sural nerve	UBERON:0015488	79.93	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.71	gold quality
blood	UBERON:0000178	79.41	gold quality
ventricular zone	UBERON:0003053	79.33	gold quality
bone marrow cell	CL:0002092	79.27	gold quality
caudate nucleus	UBERON:0001873	78.49	gold quality
adrenal tissue	UBERON:0018303	78.44	gold quality
calcaneal tendon	UBERON:0003701	78.38	gold quality
hypothalamus	UBERON:0001898	78.31	gold quality
adenohypophysis	UBERON:0002196	77.80	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.24

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300)

Protein

Protein identifiers

Zinc finger protein 487 — B1APH4 (reviewed: B1APH4)

Alternative names: KRAB domain only protein 1

All UniProt accessions (4): B1APH4, A0A494C0H0, B2REC8, H0Y2R6

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_001342373, NP_001342374, NP_001342375, NP_001342376, NP_001342377, NP_001342378, NP_001342379 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

UniProt features (4 total): chain 1, domain 1, zinc finger region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B1APH4-F1	37.79	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 25 (showing top): CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, OSMAN_BLADDER_CANCER_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CIITA_TARGET_GENES, FOXJ2_TARGET_GENES, FOXN3_TARGET_GENES, HOXA10_TARGET_GENES, ZSCAN31_TARGET_GENES, SAFB2_TARGET_GENES, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_MUSCLE_MEGAKARYOCYTES

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 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), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

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
nucleic acid binding	1
cation binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

188 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF487	OR4F21	O95013	581
ZNF487	GARIN5A	Q6IPT2	570
ZNF487	ZNF772	Q68DY9	512
ZNF487	H7C0V5	H7C0V5	507
ZNF487	RNF208	Q9H0X6	475
ZNF487	ZBTB45	Q96K62	447
ZNF487	M0QY95	M0QY95	447
ZNF487	ZNF212	Q9UDV6	446
ZNF487	ZNF816	Q0VGE8	444
ZNF487	ZNF200	P98182	444
ZNF487	SWSAP1	Q6NVH7	432
ZNF487	ZNF791	Q3KP31	431
ZNF487	ZNF101	Q8IZC7	417
ZNF487	KLHDC7B	Q96G42	400
ZNF487	ZNF488	Q96MN9	377

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ECE1	ZNF487	psi-mi:“MI:0915”(physical association)	0.370
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0JPL0, A1KXM5, A3CEM4, A6NK53, A7KBS4, A7MBI1, A8K554, A8MT65, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E7ETH6, E9Q8G5, F4KIH4, G3X9G7, O14628, P0CH99, P0CI00, P18853, Q32L17, Q3MJ40, Q3URS2, Q49AA0, Q4V8E9, Q5EBM4, Q5FWF6, Q5RE50, Q5REN4, Q6V9R5, Q6ZN11, Q6ZN79, Q755V9, Q80VJ6, Q86TJ5, Q8BGV5, Q8N535, Q8N720, Q8N859, Q8NC26

Diamond homologs: A0JPL0, A2VDP4, A6QLU5, A6QPT6, A8MQ14, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, P08042, P0CH99, P0CI00, P17014, P17025, P17030, P17031, P17032, P17098, P21506, P51508, P51523, P51786, P51814, P52736, P52738, Q02525, Q03923, Q03936, Q06730, Q06732, Q0VCB0, Q13401, Q14587, Q16587, Q2M218, Q2M3X9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1382 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000049425 (10:43451844 C>T), RS1000128833 (10:43449251 A>G), RS1000154188 (10:43485361 A>C), RS1000158832 (10:43498697 C>T), RS1000182728 (10:43435424 G>C), RS1000285556 (10:43456849 G>A), RS1000367180 (10:43462576 C>T), RS1000409562 (10:43441245 A>C), RS1000435912 (10:43462763 T>A,C), RS1000442527 (10:43482059 C>A), RS1000454411 (10:43492127 T>C), RS1000545827 (10:43477314 C>T), RS1000549815 (10:43455593 G>A), RS1000560959 (10:43457789 G>A), RS1000569973 (10:43442593 G>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

3 associations (top):

Study	Trait	p-value
GCST008891_10	Cognitive performance (processing speed)	4.000000e-06
GCST90002400_703	Plateletcrit	6.000000e-14
GCST90002402_115	Platelet count	6.000000e-12

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004363	information processing speed
EFO:0007985	platelet crit
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
beta-lapachone	decreases expression	1
perfluorooctanoic acid	increases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
Acrolein	decreases expression, increases abundance, affects cotreatment	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Ethanol	affects cotreatment, increases expression	1
Folic Acid	increases expression, affects cotreatment	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	increases methylation	1
Gold Compounds	decreases expression	1
Cadmium Chloride	decreases expression	1
Volatile Organic Compounds	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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