ZFP92

Summary

ZFP92 (ZFP92 zinc finger protein, HGNC:12865) is a protein-coding gene on chromosome Xq28, encoding Zinc finger protein 92 homolog (A6NM28). KRAB domain-containing zinc-finger protein that represses B1/Alu SINE transposable elements and modulates the transcription of nearby genes in a tissue-specific manner.

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

Source: NCBI Gene 139735 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_001136273

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12865
Approved symbol	ZFP92
Name	ZFP92 zinc finger protein
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	ZNF897
Ensembl gene	ENSG00000189420
Ensembl biotype	protein_coding
OMIM	301139
Entrez	139735

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000338647, ENST00000881745

RefSeq mRNA: 4 — MANE Select: NM_001136273 NM_001136273, NM_001386943, NM_001386944, NM_001386945

CCDS: CCDS59177

Canonical transcript exons

ENST00000338647 — 6 exons

Exon	Start	End
ENSE00001376937	153418673	153418799
ENSE00001452151	153418305	153418355
ENSE00001805277	153420228	153420332
ENSE00002593900	153420643	153426481
ENSE00003921315	153411965	153412013
ENSE00003922464	153411472	153411703

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 86.04.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	86.04	silver quality
epithelial cell of pancreas	CL:0000083	85.57	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.91	gold quality
Brodmann (1909) area 23	UBERON:0013554	77.66	gold quality
kidney epithelium	UBERON:0004819	77.48	gold quality
lower lobe of lung	UBERON:0008949	77.29	silver quality
endothelial cell	CL:0000115	76.59	gold quality
tibialis anterior	UBERON:0001385	76.44	silver quality
cardiac muscle of right atrium	UBERON:0003379	75.74	gold quality
left ventricle myocardium	UBERON:0006566	75.71	gold quality
germinal epithelium of ovary	UBERON:0001304	75.01	silver quality
cardia of stomach	UBERON:0001162	74.86	silver quality
gingival epithelium	UBERON:0001949	74.80	gold quality
entorhinal cortex	UBERON:0002728	74.19	silver quality
superior frontal gyrus	UBERON:0002661	74.15	gold quality
caput epididymis	UBERON:0004358	74.00	gold quality
myocardium	UBERON:0002349	73.89	gold quality
postcentral gyrus	UBERON:0002581	73.81	gold quality
ventral tegmental area	UBERON:0002691	73.73	silver quality
nasal cavity epithelium	UBERON:0005384	73.62	gold quality
heart right ventricle	UBERON:0002080	73.40	gold quality
parietal lobe	UBERON:0001872	73.39	gold quality
quadriceps femoris	UBERON:0001377	73.30	gold quality
vena cava	UBERON:0004087	72.90	silver quality
superficial temporal artery	UBERON:0001614	72.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.83	silver quality
vastus lateralis	UBERON:0001379	72.83	gold quality
superior vestibular nucleus	UBERON:0007227	72.07	gold quality
cauda epididymis	UBERON:0004360	72.03	gold quality
primary visual cortex	UBERON:0002436	71.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.74

Regulation

Is transcription factor: no

Cross-species orthologs

18 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf646	ENSDARG00000061424
danio_rerio	si:dkey-154p10.3	ENSDARG00000068366
danio_rerio	si:dkey-89b17.4	ENSDARG00000075545
danio_rerio	zgc:66472	ENSDARG00000075916
danio_rerio	si:ch211-148l7.4	ENSDARG00000094469
danio_rerio	znf576.1	ENSDARG00000097819
mus_musculus	Zfp92	ENSMUSG00000031374
rattus_norvegicus	Zfp92	ENSRNOG00000051836
drosophila_melanogaster	az2	FBGN0025185
drosophila_melanogaster	CG2129	FBGN0030008
drosophila_melanogaster	CG1602	FBGN0033186
drosophila_melanogaster	CG18011	FBGN0033491
drosophila_melanogaster	CG12942	FBGN0033569
drosophila_melanogaster	indra	FBGN0035213
drosophila_melanogaster	CG30020	FBGN0050020
drosophila_melanogaster	mld	FBGN0263490
caenorhabditis_elegans	ztf-15	WBGENE00011066
caenorhabditis_elegans		WBGENE00015649

Paralogs (36): ZNF302 (ENSG00000089335), ZNF184 (ENSG00000096654), CTCF (ENSG00000102974), ZNF574 (ENSG00000105732), ZBTB24 (ENSG00000112365), ZNF142 (ENSG00000115568), CTCFL (ENSG00000124092), ZNF473 (ENSG00000142528), ZNF827 (ENSG00000151612), ZNF689 (ENSG00000156853), ZNF208 (ENSG00000160321), ZNF91 (ENSG00000167232), ZNF526 (ENSG00000167625), ZNF764 (ENSG00000169951), ZNF747 (ENSG00000169955), ZNF282 (ENSG00000170265), ZNF160 (ENSG00000170949), ZNF497 (ENSG00000174586), ZBTB34 (ENSG00000177125), ZNF771 (ENSG00000179965), ZNF48 (ENSG00000180035), ZNF594 (ENSG00000180626), ZBTB37 (ENSG00000185278), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF569 (ENSG00000196437), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZNF84 (ENSG00000198040), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973), ZNF688 (ENSG00000229809)

Protein

Protein identifiers

Zinc finger protein 92 homolog — A6NM28 (reviewed: A6NM28)

All UniProt accessions (1): A6NM28

UniProt curated annotations — full annotation on UniProt →

Function. KRAB domain-containing zinc-finger protein that represses B1/Alu SINE transposable elements and modulates the transcription of nearby genes in a tissue-specific manner. It regulates glucose homeostasis and lipid metabolism by modulating the expression of the endocrine cell-defining transcription factor, MAFB, in pancreatic islets and, the fat metabolism regulator, ACACB, in adipose tissue and muscle.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

RefSeq proteins (4): NP_001129745, NP_001373872, NP_001373873, NP_001373874 (=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

Pfam: PF00096, PF01352

UniProt features (15 total): zinc finger region 8, region of interest 2, sequence conflict 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NM28-F1	72.67	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): GOBP_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOBP_REGULATION_OF_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_REGULATION_OF_GLUCOSE_METABOLIC_PROCESS, GOBP_GLUCOSE_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_MONOSACCHARIDE_METABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, chrXq28, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, GOBP_TRANSPOSITION, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOBP_REGULATION_OF_SMALL_MOLECULE_METABOLIC_PROCESS

GO Biological Process (6): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), transposable element silencing (GO:0010526), regulation of glucose metabolic process (GO:0010906), regulation of lipid metabolic process (GO:0019216), regulation of DNA-templated transcription (GO:0006355)

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), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), DNA binding (GO:0003677), 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	3
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of gene expression	1
retrotransposition	1
glucose metabolic process	1
regulation of carbohydrate metabolic process	1
regulation of small molecule metabolic process	1
lipid metabolic process	1
regulation of primary metabolic process	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
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

98 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFP92	ANKRD35	Q8N283	507
ZFP92	TARBP1	Q13395	445
ZFP92	SLC38A12	Q8NE00	351
ZFP92	EARS2	Q5JPH6	343
ZFP92	LHX9	Q9NQ69	310
ZFP92	INSL3	P51460	293
ZFP92	ZFPM2	Q8WW38	267
ZFP92	ECT2	Q9H8V3	248
ZFP92	AMFR	P26442	247
ZFP92	NRIP1	P48552	236
ZFP92	TBC1D8	O95759	222
ZFP92	NR0B1	P51843	219
ZFP92	NR5A1	Q13285	203
ZFP92	URI1	O94763	194
ZFP92	HLA-DRA	P01903	187

IntAct

0 interactions, top by confidence:

BioGRID (2): ZFP92 (Affinity Capture-MS), ZFP92 (Affinity Capture-MS)

ESM2 similar proteins: A2CE44, A6NFI3, A6NM28, A8K8V0, O15370, O70218, O95201, P0CJ78, P10075, P10754, P28698, P70338, Q04890, Q07120, Q14V87, Q19A40, Q569E7, Q58DK7, Q5DWN0, Q5FWU5, Q5RJR4, Q5T619, Q5TEC3, Q6DD87, Q6IQX8, Q6PD29, Q6PGE4, Q6ZMY9, Q7Z7K2, Q80VM4, Q8BIF9, Q8JZL0, Q8N8E2, Q8NAF0, Q8NCA9, Q8TD94, Q8WUU4, Q96C55, Q96H86, Q96MX3

Diamond homologs: A0JPL0, A2A761, A3KN32, A3KN36, A6NFI3, A6NM28, A6QLU5, A6QPT6, A7MBI1, A8MTY0, B2RXC5, B4DU55, E9PYI1, O14978, O60765, O75467, O75820, O95780, P0C7X2, P0DKX0, P0DPD5, P10072, P15622, P16374, P17014, P17023, P17032, P17098, P51523, P51786, P52738, P52742, Q02975, Q06732, Q08DG8, Q08ER8, Q0VCB0, Q14590, Q14929, Q29RZ4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

451 predictions. Top by Δscore:

Variant	Effect	Δscore
X:153418797:TGGG:T	donor_loss	1.0000
X:153418798:GG:G	donor_gain	1.0000
X:153418798:GGGT:G	donor_loss	1.0000
X:153418799:GG:G	donor_gain	1.0000
X:153418800:G:GG	donor_gain	1.0000
X:153418801:TAAG:T	donor_loss	1.0000
X:153418352:CAAGG:C	donor_loss	0.9900
X:153418353:AAGG:A	donor_loss	0.9900
X:153418354:AGG:A	donor_loss	0.9900
X:153418355:GGTG:G	donor_loss	0.9900
X:153418356:G:GG	donor_gain	0.9900
X:153418356:GTG:G	donor_loss	0.9900
X:153418357:T:A	donor_loss	0.9900
X:153418795:ACTGG:A	donor_gain	0.9900
X:153418796:CTGG:C	donor_gain	0.9900
X:153418797:TGG:T	donor_gain	0.9900
X:153418798:GGG:G	donor_gain	0.9900
X:153420638:TCCA:T	acceptor_loss	0.9900
X:153420641:A:AG	acceptor_gain	0.9900
X:153420641:AG:A	acceptor_gain	0.9900
X:153420641:AGGT:A	acceptor_gain	0.9900
X:153420642:G:GG	acceptor_gain	0.9900
X:153420642:GG:G	acceptor_gain	0.9900
X:153420642:GGT:G	acceptor_gain	0.9900
X:153420642:GGTG:G	acceptor_gain	0.9900
X:153418668:TTTA:T	acceptor_loss	0.9800
X:153418669:TTAG:T	acceptor_loss	0.9800
X:153418670:TAG:T	acceptor_loss	0.9800
X:153418671:A:AT	acceptor_loss	0.9800
X:153420641:AGG:A	acceptor_gain	0.9800

AlphaMissense

2713 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:153421026:T:C	F217L	0.999
X:153421028:C:A	F217L	0.999
X:153421028:C:G	F217L	0.999
X:153421194:T:C	F273L	0.999
X:153421196:C:A	F273L	0.999
X:153421196:C:G	F273L	0.999
X:153421278:T:C	F301L	0.999
X:153421280:C:A	F301L	0.999
X:153421280:C:G	F301L	0.999
X:153421446:T:C	F357L	0.999
X:153421448:C:A	F357L	0.999
X:153421448:C:G	F357L	0.999
X:153420858:T:C	F161L	0.998
X:153420860:C:A	F161L	0.998
X:153420860:C:G	F161L	0.998
X:153421213:T:C	L279P	0.998
X:153421223:C:A	H282Q	0.998
X:153421223:C:G	H282Q	0.998
X:153421305:C:A	H310N	0.998
X:153421362:T:C	F329L	0.998
X:153421364:C:A	F329L	0.998
X:153421364:C:G	F329L	0.998
X:153420971:C:A	H198Q	0.997
X:153420971:C:G	H198Q	0.997
X:153421194:T:A	F273I	0.997
X:153421195:T:C	F273S	0.997
X:153421305:C:G	H310D	0.997
X:153421307:C:A	H310Q	0.997
X:153421307:C:G	H310Q	0.997
X:153421335:T:C	F320L	0.997

dbSNP variants (sampled 300 via entrez): RS1000091561 (X:153417687 T>C), RS1000193816 (X:153411401 C>T), RS1001226417 (X:153425226 C>A,T), RS1001325058 (X:153417969 G>A), RS1001339850 (X:153422623 C>T), RS1001836334 (X:153411921 G>A,C,T), RS1002310811 (X:153416884 C>A,T), RS1002619867 (X:153423555 T>C), RS1003000065 (X:153418977 G>C), RS1003104422 (X:153413610 T>A,C), RS1003303071 (X:153426816 G>A), RS1004020795 (X:153423271 G>A), RS1004236665 (X:153424958 C>T), RS1004678106 (X:153417104 T>C), RS1005076890 (X:153422076 G>A)

Disease associations

OMIM: gene MIM:301139 | 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

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects response to substance, increases expression, affects methylation	2
triphenyl phosphate	affects expression	1
sulforaphane	increases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
Acetaminophen	decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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