ZNF135

Summary

ZNF135 (zinc finger protein 135, HGNC:12919) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 135 (P52742). Plays a role in the regulation of cell morphology and cytoskeletal organization.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cytoskeleton organization and regulation of cell morphogenesis. Predicted to be active in nucleus.

Source: NCBI Gene 7694 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 114 total
• MANE Select transcript: NM_001289401

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12919
Approved symbol	ZNF135
Name	zinc finger protein 135
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	pHZ-17
Ensembl gene	ENSG00000176293
Ensembl biotype	protein_coding
OMIM	604077
Entrez	7694

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 nonsense_mediated_decay

ENST00000313434, ENST00000359978, ENST00000401053, ENST00000506786, ENST00000511556, ENST00000515535, ENST00000890101, ENST00000890102, ENST00000890103, ENST00000890104, ENST00000938056

RefSeq mRNA: 7 — MANE Select: NM_001289401 NM_001164527, NM_001164529, NM_001164530, NM_001289401, NM_001289402, NM_003436, NM_007134

CCDS: CCDS12970, CCDS54329, CCDS54330, CCDS74471, CCDS74472

Canonical transcript exons

ENST00000313434 — 5 exons

Exon	Start	End
ENSE00001353570	58059969	58060035
ENSE00001353577	58059282	58059310
ENSE00001719254	58063446	58063541
ENSE00002019607	58066741	58069755
ENSE00003584871	58061580	58061706

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 89.09.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5642 / max 45.8352, expressed in 652 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177811	1.3989	606
208950	0.1653	85

Top tissues by expression

283 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	89.09	gold quality
ganglionic eminence	UBERON:0004023	85.29	gold quality
cortical plate	UBERON:0005343	84.11	gold quality
endothelial cell	CL:0000115	83.52	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.57	gold quality
left ovary	UBERON:0002119	79.79	gold quality
ventricular zone	UBERON:0003053	79.58	gold quality
right lobe of thyroid gland	UBERON:0001119	78.77	gold quality
right ovary	UBERON:0002118	78.29	gold quality
right uterine tube	UBERON:0001302	78.12	gold quality
left lobe of thyroid gland	UBERON:0001120	77.96	gold quality
thyroid gland	UBERON:0002046	76.99	gold quality
ovary	UBERON:0000992	76.79	gold quality
body of uterus	UBERON:0009853	76.78	gold quality
apex of heart	UBERON:0002098	76.16	gold quality
adenohypophysis	UBERON:0002196	75.63	gold quality
stromal cell of endometrium	CL:0002255	75.53	gold quality
pituitary gland	UBERON:0000007	75.43	gold quality
endocervix	UBERON:0000458	75.17	gold quality
left uterine tube	UBERON:0001303	75.05	gold quality
right coronary artery	UBERON:0001625	74.68	gold quality
ectocervix	UBERON:0012249	74.54	gold quality
lower esophagus muscularis layer	UBERON:0035833	74.40	gold quality
lower esophagus	UBERON:0013473	74.36	gold quality
popliteal artery	UBERON:0002250	74.17	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.17	gold quality
tibial artery	UBERON:0007610	74.16	gold quality
hair follicle	UBERON:0002073	74.15	gold quality
right testis	UBERON:0004534	74.11	gold quality
islet of Langerhans	UBERON:0000006	74.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.22

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
CADM1
CDKN2A

JASPAR motifs

Motif	Name	Family
MA1587.1	ZNF135	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28092692

miRNA regulators (miRDB)

47 targeting ZNF135, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-4762-5P	99.57	68.54	1424
HSA-MIR-182-3P	99.57	67.57	825
HSA-MIR-6716-5P	99.56	68.62	1244
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-135A-5P	99.36	71.85	1601
HSA-MIR-135B-5P	99.36	71.63	1613
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-12135	98.99	70.26	1814
HSA-MIR-629-5P	98.78	68.72	1032

Cross-species orthologs

0 orthologs

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 135 — P52742 (reviewed: P52742)

Alternative names: Zinc finger protein 61, Zinc finger protein 78-like 1

All UniProt accessions (3): P52742, M0R0N7, Q8N9M3

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the regulation of cell morphology and cytoskeletal organization. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Miscellaneous. May be due to competing acceptor splice site.

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

Isoforms (4)

UniProt ID	Names	Canonical?
P52742-1	1	yes
P52742-2	2
P52742-3	3
P52742-4	4

RefSeq proteins (7): NP_001157999, NP_001158001, NP_001158002, NP_001276330, NP_001276331, NP_003427, NP_009065 (=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 (30 total): zinc finger region 16, sequence variant 5, splice variant 3, sequence conflict 3, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P52742-F1	73.59	0.31

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 101 (showing top): GOBP_REGULATION_OF_CELL_MORPHOGENESIS, BROWNE_HCMV_INFECTION_48HR_DN, BROWNE_HCMV_INFECTION_14HR_DN, MULLIGHAN_NPM1_SIGNATURE_3_DN, GRADE_COLON_AND_RECTAL_CANCER_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN, BAE_BRCA1_TARGETS_DN, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, E2F3_UP.V1_DN, SRC_UP.V1_DN, NFE2L2.V2, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR570_3P, MIR4795_3P

GO Biological Process (6): regulation of transcription by RNA polymerase II (GO:0006357), cytoskeleton organization (GO:0007010), regulation of cell morphogenesis (GO:0022604), regulation of DNA-templated transcription (GO:0006355), regulation of anatomical structure morphogenesis (GO:0022603), negative regulation of DNA-templated transcription (GO:0045892)

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)

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
regulation of DNA-templated transcription	2
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
organelle organization	1
cell morphogenesis	1
regulation of anatomical structure morphogenesis	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
anatomical structure morphogenesis	1
regulation of developmental process	1
negative 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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF135	MAGEB10	Q96LZ2	398
ZNF135	ITPRID1	Q6ZRS4	372
ZNF135	GPATCH2L	Q9NWQ4	351
ZNF135	ADHFE1	Q8IWW8	318
ZNF135	MAGEB3	O15480	317
ZNF135	LRRIQ1	Q96JM4	302
ZNF135	MYO15B	Q96JP2	300
ZNF135	HTATIP2	Q9BUP3	290
ZNF135	EML3	Q32P44	290
ZNF135	CARD8	Q9Y2G2	290
ZNF135	PPP1R3E	Q9H7J1	289
ZNF135	TMEM25	Q86YD3	272
ZNF135	CCDC124	Q96CT7	272
ZNF135	MAGEF1	Q9HAY2	271
ZNF135	MAGEB18	Q96M61	270
ZNF135	FAM163A	Q96GL9	270

IntAct

20 interactions, top by confidence:

A	B	Type	Score
ZNF135	LMO4	psi-mi:“MI:0915”(physical association)	0.560
ZNF135	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
ZNF135	ANKS1A	psi-mi:“MI:0915”(physical association)	0.560
ZNF135	WWOX	psi-mi:“MI:0915”(physical association)	0.560
ZNF135		psi-mi:“MI:0915”(physical association)	0.370
ANXA7	ZNF135	psi-mi:“MI:0915”(physical association)	0.370
ZNF135	CDKN1A	psi-mi:“MI:0915”(physical association)	0.370
ZNF135	GADD45A	psi-mi:“MI:0915”(physical association)	0.370
GSK3B	ZNF135	psi-mi:“MI:0915”(physical association)	0.370
ZNF135	RAP1B	psi-mi:“MI:0915”(physical association)	0.370
ZNF135	RCC1	psi-mi:“MI:0915”(physical association)	0.370
WWOX	ZNF135	psi-mi:“MI:0915”(physical association)	0.000
LMO4	ZNF135	psi-mi:“MI:0915”(physical association)	0.000
SCNM1	ZNF135	psi-mi:“MI:0915”(physical association)	0.000
ANKS1A	ZNF135	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): ZNF135 (Two-hybrid), ZNF135 (Two-hybrid), ZNF135 (Two-hybrid), WWOX (Two-hybrid), ZNF135 (Affinity Capture-RNA), ZNF135 (Two-hybrid), ZNF135 (Two-hybrid), ZNF135 (Two-hybrid), ZNF135 (Two-hybrid), ZNF135 (Two-hybrid), ZNF135 (Two-hybrid)

ESM2 similar proteins: A2VDQ7, A6NN14, A8MQ14, A8MTY0, B7Z6K7, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17035, P17039, P18745, P18751, P35789, P51522, P51523, P52742, Q02386, Q08AN1, Q14585, Q14587, Q3SYV7, Q4R4C7, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6P5C7, Q6ZN06, Q6ZN57, Q86UE3, Q86XN6, Q8IYB9, Q8N4W9, Q8N7M2, Q8N7Q3, Q8N972

Diamond homologs: A0JPL0, A1L1L7, A2A761, A2VDP4, A3KN36, A6QLU5, A6QPT6, A7MBI1, A8MT65, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, O95780, P10076, P17014, P17023, P17025, P17030, P17032, P17098, P51523, P51814, P52736, P52742, P58317, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14584, Q14587, Q14590, Q147U1, Q16587, Q29RZ4, Q2M218

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	94
Likely benign	5
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

1172 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58061702:TGTGG:T	donor_loss	1.0000
19:58061703:GTGG:G	donor_gain	1.0000
19:58061705:GG:G	donor_gain	1.0000
19:58061705:GGGT:G	donor_loss	1.0000
19:58061706:GG:G	donor_gain	1.0000
19:58061706:GGTAA:G	donor_loss	1.0000
19:58061707:G:GC	donor_loss	1.0000
19:58061708:TAA:T	donor_loss	1.0000
19:58086168:CCTCA:C	donor_loss	1.0000
19:58086169:CTCA:C	donor_loss	1.0000
19:58086170:TCA:T	donor_loss	1.0000
19:58086171:CAC:C	donor_loss	1.0000
19:58086187:T:TA	donor_gain	1.0000
19:58086262:ATACC:A	acceptor_gain	1.0000
19:58086263:TACC:T	acceptor_gain	1.0000
19:58086264:ACC:A	acceptor_gain	1.0000
19:58086264:ACCC:A	acceptor_loss	1.0000
19:58086265:CC:C	acceptor_gain	1.0000
19:58086265:CCC:C	acceptor_gain	1.0000
19:58086266:CC:C	acceptor_gain	1.0000
19:58086267:C:CC	acceptor_gain	1.0000
19:58086267:C:T	acceptor_gain	1.0000
19:58086271:G:C	acceptor_gain	1.0000
19:58086271:G:GC	acceptor_gain	1.0000
19:58086276:G:C	acceptor_gain	1.0000
19:58086276:G:GC	acceptor_gain	1.0000
19:58086277:T:C	acceptor_gain	1.0000
19:58086277:T:TC	acceptor_gain	1.0000
19:58086285:C:CT	acceptor_gain	1.0000
19:58059306:GGAGG:G	donor_gain	0.9900

AlphaMissense

4378 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:58067487:T:C	F335L	0.999
19:58067489:C:A	F335L	0.999
19:58067489:C:G	F335L	0.999
19:58067571:T:C	F363L	0.999
19:58067573:C:A	F363L	0.999
19:58067573:C:G	F363L	0.999
19:58067655:T:C	F391L	0.999
19:58067657:C:A	F391L	0.999
19:58067657:C:G	F391L	0.999
19:58067739:T:C	F419L	0.999
19:58067741:C:A	F419L	0.999
19:58067741:C:G	F419L	0.999
19:58067403:T:C	F307L	0.998
19:58067405:C:A	F307L	0.998
19:58067405:C:G	F307L	0.998
19:58067506:T:C	L341P	0.998
19:58067516:T:A	H344Q	0.998
19:58067516:T:G	H344Q	0.998
19:58067605:G:C	R374P	0.998
19:58067907:T:C	F475L	0.998
19:58067909:C:A	F475L	0.998
19:58067909:C:G	F475L	0.998
19:58067991:T:C	F503L	0.998
19:58067993:C:A	F503L	0.998
19:58067993:C:G	F503L	0.998
19:58068159:T:C	F559L	0.998
19:58068161:C:A	F559L	0.998
19:58068161:C:G	F559L	0.998
19:58067235:T:C	F251L	0.997
19:58067237:C:A	F251L	0.997

dbSNP variants (sampled 300 via entrez): RS1000007384 (19:58062497 C>G,T), RS1000038573 (19:58062733 C>T), RS1000100401 (19:58062260 C>G,T), RS1001012788 (19:58069879 T>C), RS1001044296 (19:58066522 T>C), RS1001052817 (19:58058220 G>A,C), RS1001677741 (19:58060863 G>A), RS1001710686 (19:58061086 C>T), RS1002201440 (19:58066049 A>G), RS1002232334 (19:58066262 C>T), RS1003239205 (19:58064697 T>A), RS1003392654 (19:58059809 C>A,G), RS1003487903 (19:58059541 A>G), RS1003812937 (19:58062865 A>C), RS1004155942 (19:58057245 T>C)

Disease associations

OMIM: gene MIM:604077 | 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

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases methylation	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
Resveratrol	increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Bucladesine	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, increases expression	1
Niclosamide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Medroxyprogesterone Acetate	affects cotreatment, increases expression	1
Sodium Selenite	decreases expression	1
Cadmium Chloride	increases abundance, decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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