ZNF169

Summary

ZNF169 (zinc finger protein 169, HGNC:12957) is a protein-coding gene on chromosome 9q22.32, encoding Zinc finger protein 169 (Q14929). 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 active in nucleus.

Source: NCBI Gene 169841 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 90 total
• MANE Select transcript: NM_194320

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12957
Approved symbol	ZNF169
Name	zinc finger protein 169
Location	9q22.32
Locus type	gene with protein product
Status	Approved
Aliases	MGC51961
Ensembl gene	ENSG00000175787
Ensembl biotype	protein_coding
OMIM	603404
Entrez	169841

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 retained_intron

ENST00000340911, ENST00000395395, ENST00000480716, ENST00000481550, ENST00000492115, ENST00000718459, ENST00000718460, ENST00000873354, ENST00000873355, ENST00000873356

RefSeq mRNA: 3 — MANE Select: NM_194320 NM_001301275, NM_003448, NM_194320

CCDS: CCDS6709

Canonical transcript exons

ENST00000395395 — 5 exons

Exon	Start	End
ENSE00001421123	94299815	94301829
ENSE00001853948	94259298	94259345
ENSE00003548741	94292341	94292467
ENSE00003616200	94278758	94278845
ENSE00003672045	94292974	94293069

Expression profiles

Bgee: expression breadth ubiquitous, 219 present calls, max score 89.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.2778 / max 29.2792, expressed in 1148 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97453	2.2778	1148

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	89.75	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.80	gold quality
monocyte	CL:0000576	80.21	gold quality
subthalamic nucleus	UBERON:0001906	80.14	gold quality
cardia of stomach	UBERON:0001162	79.77	gold quality
leukocyte	CL:0000738	79.70	gold quality
rectum	UBERON:0001052	79.54	gold quality
lateral nuclear group of thalamus	UBERON:0002736	78.33	silver quality
dorsal plus ventral thalamus	UBERON:0001897	77.85	gold quality
lateral globus pallidus	UBERON:0002476	77.80	silver quality
right uterine tube	UBERON:0001302	77.02	gold quality
right ovary	UBERON:0002118	76.73	gold quality
left ovary	UBERON:0002119	76.58	gold quality
inferior vagus X ganglion	UBERON:0005363	76.41	gold quality
vena cava	UBERON:0004087	76.18	silver quality
endocervix	UBERON:0000458	76.14	gold quality
prefrontal cortex	UBERON:0000451	76.12	gold quality
ventral tegmental area	UBERON:0002691	76.08	gold quality
small intestine Peyer’s patch	UBERON:0003454	76.03	gold quality
lymph node	UBERON:0000029	75.88	gold quality
body of uterus	UBERON:0009853	75.77	gold quality
right coronary artery	UBERON:0001625	75.65	gold quality
tibial nerve	UBERON:0001323	75.58	gold quality
right lobe of thyroid gland	UBERON:0001119	75.48	gold quality
trachea	UBERON:0003126	75.48	gold quality
transverse colon	UBERON:0001157	75.44	gold quality
ectocervix	UBERON:0012249	75.41	gold quality
saliva-secreting gland	UBERON:0001044	75.35	gold quality
substantia nigra pars compacta	UBERON:0001965	75.26	gold quality
metanephros cortex	UBERON:0010533	75.25	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.99

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

14 targeting ZNF169, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-8062	99.88	68.43	995
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-4753-5P	99.54	68.51	1356
HSA-MIR-154-5P	98.92	66.65	733
HSA-MIR-1245B-5P	98.88	66.55	576
HSA-MIR-3142	98.88	66.09	529
HSA-MIR-3611	98.76	68.76	1290
HSA-MIR-4733-3P	98.35	65.20	994
HSA-MIR-6849-3P	97.25	64.57	1371

Literature-anchored findings (GeneRIF, showing 1)

• Overexpression of ZNF169 promotes the growth and proliferation of colorectal cancer cells via the upregulation of ANKZF1. (PMID:38666541)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp169	ENSMUSG00000050954
rattus_norvegicus	Zfp169	ENSRNOG00000017092
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

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), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 169 — Q14929 (reviewed: Q14929)

All UniProt accessions (4): Q14929, Q5SR55, Q7Z761, S4R440

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in kidney, weakly expressed in heart, liver, spleen, and small intestine. Not expressed in adult brain or spinal cord.

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

RefSeq proteins (3): NP_001288204, NP_003439, NP_919301* (*=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 (30 total): zinc finger region 13, sequence conflict 7, sequence variant 5, region of interest 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14929-F1	72.11	0.41

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 54 (showing top): chr9q22, URS_ADIPOCYTE_DIFFERENTIATION_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, DLX4_TARGET_GENES, DMRT1_TARGET_GENES, ELF2_TARGET_GENES, FEV_TARGET_GENES, PAX3_TARGET_GENES, SUPT16H_TARGET_GENES, ZSCAN2_TARGET_GENES, MIR3941, MIR6876_5P, MIR4476

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

GO Molecular Function (6): 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), 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	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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

628 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF169	ASS1	P00966	750
ZNF169	FANCC	Q00597	624
ZNF169	XPA	P23025	581
ZNF169	TGFBR1	P36897	574
ZNF169	PTCH1	Q13635	529
ZNF169	ATP13A4	Q4VNC1	508
ZNF169	NUTM2G	Q5VZR2	473
ZNF169	SLC67A1	Q96BI1	457
ZNF169	GJA10	Q969M2	452
ZNF169	SLC38A4	Q969I6	449
ZNF169	HHAT	Q5VTY9	449
ZNF169	NUTM2F	A1L443	448
ZNF169	CFAP210	Q0VFZ6	448
ZNF169	DUSP22	Q9NRW4	441
ZNF169	AGPAT2	O15120	432

IntAct

19 interactions, top by confidence:

A	B	Type	Score
CCNDBP1	ZNF169	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF169	psi-mi:“MI:0915”(physical association)	0.560
ZNF169	CEP70	psi-mi:“MI:0915”(physical association)	0.560
ZNF169	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.560
ZNF169	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-6	ZNF169	psi-mi:“MI:0915”(physical association)	0.560
ZNF169	CABP5	psi-mi:“MI:0915”(physical association)	0.560
ZNF169	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF169	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000
CABP5	ZNF169	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (85): ZNF169 (Two-hybrid), ZNF169 (Two-hybrid), KRTAP10-7 (Two-hybrid), ZNF169 (Affinity Capture-MS), C10orf2 (Affinity Capture-MS), RBAK (Affinity Capture-MS), SOGA1 (Affinity Capture-MS), ZYG11A (Affinity Capture-MS), ZNF92 (Affinity Capture-MS), SORL1 (Affinity Capture-MS), ZNF689 (Affinity Capture-MS), ZBTB10 (Affinity Capture-MS), ZNF445 (Affinity Capture-MS), TRIM41 (Affinity Capture-MS), TRIM26 (Affinity Capture-MS)

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: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

819 predictions. Top by Δscore:

Variant	Effect	Δscore
9:94278754:CCAG:C	acceptor_loss	1.0000
9:94278757:GATTT:G	acceptor_gain	1.0000
9:94278842:GGAG:G	donor_gain	1.0000
9:94278843:GAG:G	donor_gain	1.0000
9:94278843:GAGG:G	donor_gain	1.0000
9:94278844:AGGTA:A	donor_loss	1.0000
9:94278845:GGTA:G	donor_loss	1.0000
9:94278846:G:GA	donor_loss	1.0000
9:94278846:G:GG	donor_gain	1.0000
9:94278847:T:A	donor_loss	1.0000
9:94292335:TTACA:T	acceptor_loss	1.0000
9:94292339:A:AG	acceptor_gain	1.0000
9:94292339:AG:A	acceptor_gain	1.0000
9:94292340:G:GT	acceptor_gain	1.0000
9:94292340:GG:G	acceptor_gain	1.0000
9:94292340:GGC:G	acceptor_gain	1.0000
9:94292340:GGCA:G	acceptor_gain	1.0000
9:94292340:GGCAT:G	acceptor_gain	1.0000
9:94292428:G:T	donor_gain	1.0000
9:94292434:A:AG	donor_gain	1.0000
9:94292466:GG:G	donor_gain	1.0000
9:94292467:GG:G	donor_gain	1.0000
9:94292468:G:A	donor_loss	1.0000
9:94292468:G:GG	donor_gain	1.0000
9:94292469:T:G	donor_loss	1.0000
9:94292965:T:TA	acceptor_gain	1.0000
9:94292967:T:TA	acceptor_gain	1.0000
9:94292971:TAGGA:T	acceptor_loss	1.0000
9:94292972:A:G	acceptor_loss	1.0000
9:94292973:G:GT	acceptor_loss	1.0000

AlphaMissense

3953 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:94300537:T:C	F327L	0.999
9:94300539:T:A	F327L	0.999
9:94300539:T:G	F327L	0.999
9:94300621:T:C	F355L	0.999
9:94300623:T:A	F355L	0.999
9:94300623:T:G	F355L	0.999
9:94300873:T:C	F439L	0.999
9:94300875:T:A	F439L	0.999
9:94300875:T:G	F439L	0.999
9:94300957:T:C	F467L	0.999
9:94300959:T:A	F467L	0.999
9:94300959:T:G	F467L	0.999
9:94300369:T:C	F271L	0.997
9:94300371:T:A	F271L	0.997
9:94300371:T:G	F271L	0.997
9:94300453:T:C	F299L	0.997
9:94300455:C:A	F299L	0.997
9:94300455:C:G	F299L	0.997
9:94300789:T:C	F411L	0.997
9:94300791:T:A	F411L	0.997
9:94300791:T:G	F411L	0.997
9:94300874:T:C	F439S	0.997
9:94300538:T:C	F327S	0.996
9:94300705:T:C	F383L	0.996
9:94300707:C:A	F383L	0.996
9:94300707:C:G	F383L	0.996
9:94300734:C:A	H392Q	0.996
9:94300734:C:G	H392Q	0.996
9:94300892:T:C	L445P	0.996
9:94300902:C:A	H448Q	0.996

dbSNP variants (sampled 300 via entrez): RS1000223284 (9:94269146 T>C), RS1000264404 (9:94260982 G>A), RS1000273346 (9:94276580 A>G), RS1000488597 (9:94282226 T>G), RS1000506612 (9:94268206 A>G), RS1000607420 (9:94274864 C>T), RS1000698369 (9:94260711 G>A), RS1000737627 (9:94273984 A>C), RS1000744311 (9:94277718 T>G), RS1000845877 (9:94298685 C>T), RS1000874510 (9:94263089 T>A,C), RS1000938007 (9:94293937 G>A), RS1001024954 (9:94273780 C>T), RS1001038723 (9:94294443 GA>G,GAA), RS1001137898 (9:94258123 C>G,T)

Disease associations

OMIM: gene MIM:603404 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001416_9	Body mass index (SNP x SNP interaction)	6.000000e-07
GCST004904_45	Body mass index	3.000000e-09
GCST004904_63	Body mass index	2.000000e-09
GCST006222_3	Cerebellum growth	1.000000e-06
GCST008128_5	Body mass index	9.000000e-10
GCST009379_90	Type 2 diabetes	2.000000e-09
GCST009379_91	Type 2 diabetes	3.000000e-06
GCST90002396_410	Mean reticulocyte volume	4.000000e-29
GCST90002397_687	Mean spheric corpuscular volume	3.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0010701	mean reticulocyte volume

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
Tobacco Smoke Pollution	decreases expression, increases expression	2
Cadmium Chloride	decreases expression	2
TAK-243	increases sumoylation	1
bisphenol A	decreases methylation	1
(+)-JQ1 compound	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_XW11	HEK293 eGFP-ZNF169	Transformed cell line	Female

Clinical trials (associated diseases)

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