ZNF688

Summary

ZNF688 (zinc finger protein 688, HGNC:30489) is a protein-coding gene on chromosome 16p11.2, encoding Zinc finger protein 688 (P0C7X2). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 146542 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_145271

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30489
Approved symbol	ZNF688
Name	zinc finger protein 688
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000229809
Ensembl biotype	protein_coding
Entrez	146542

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 retained_intron

ENST00000223459, ENST00000562455, ENST00000563276, ENST00000563665, ENST00000563707, ENST00000566632, ENST00000567855, ENST00000897344, ENST00000897345, ENST00000897346

RefSeq mRNA: 2 — MANE Select: NM_145271 NM_001024683, NM_145271

CCDS: CCDS10684, CCDS42151

Canonical transcript exons

ENST00000223459 — 3 exons

Exon	Start	End
ENSE00000704440	30571010	30571123
ENSE00001520971	30571434	30571714
ENSE00002603306	30569726	30570436

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 90.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.3064 / max 108.5483, expressed in 1726 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157068	4.0868	1612
157069	0.9072	476
157067	0.8189	519
157070	0.4936	251

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	90.29	gold quality
buccal mucosa cell	CL:0002336	89.59	silver quality
right testis	UBERON:0004534	89.17	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.17	gold quality
apex of heart	UBERON:0002098	88.29	gold quality
left testis	UBERON:0004533	88.14	gold quality
sperm	CL:0000019	87.89	gold quality
granulocyte	CL:0000094	87.88	gold quality
male germ cell	CL:0000015	87.42	gold quality
right uterine tube	UBERON:0001302	87.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.81	gold quality
vena cava	UBERON:0004087	86.59	silver quality
mucosa of transverse colon	UBERON:0004991	86.50	gold quality
testis	UBERON:0000473	86.32	gold quality
epithelium of bronchus	UBERON:0002031	85.50	gold quality
bronchial epithelial cell	CL:0002328	85.26	gold quality
bronchus	UBERON:0002185	85.21	gold quality
prefrontal cortex	UBERON:0000451	84.98	gold quality
pancreatic ductal cell	CL:0002079	84.96	silver quality
cerebellar hemisphere	UBERON:0002245	84.81	gold quality
cerebellar cortex	UBERON:0002129	84.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.68	gold quality
leukocyte	CL:0000738	84.59	gold quality
monocyte	CL:0000576	84.58	gold quality
mononuclear cell	CL:0000842	84.50	gold quality
lower esophagus	UBERON:0013473	84.44	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.44	gold quality
gastrocnemius	UBERON:0001388	84.36	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.33	gold quality
adenohypophysis	UBERON:0002196	84.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting ZNF688, 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-4713-3P	100.00	65.92	505
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-4253	97.48	65.11	692
HSA-MIR-6862-5P	97.48	64.84	713
HSA-MIR-1293	96.16	64.69	916

Cross-species orthologs

13 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf646	ENSDARG00000061424
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	Zfp688	ENSMUSG00000045251
rattus_norvegicus	Zfp688	ENSRNOG00000018379
drosophila_melanogaster	az2	FBGN0025185
drosophila_melanogaster	CG2129	FBGN0030008
drosophila_melanogaster	CG1602	FBGN0033186
drosophila_melanogaster	indra	FBGN0035213
drosophila_melanogaster	CG30020	FBGN0050020
drosophila_melanogaster	mld	FBGN0263490

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), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF569 (ENSG00000196437), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZNF84 (ENSG00000198040), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973)

Protein

Protein identifiers

Zinc finger protein 688 — P0C7X2 (reviewed: P0C7X2)

All UniProt accessions (6): A0A0S2Z5X4, A0A0S2Z633, H3BR26, H3BR45, H3BTK8, P0C7X2

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 (2)

UniProt ID	Names	Canonical?
P0C7X2-1	1	yes
P0C7X2-5	2

RefSeq proteins (2): NP_001019854, NP_660314* (*=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
IPR050169	Krueppel_C2H2_ZnF	Family

Pfam: PF00096, PF01352

UniProt features (14 total): region of interest 3, compositionally biased region 3, sequence conflict 2, zinc finger region 2, chain 1, domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C7X2-F1	59.52	0.01

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 117 (showing top): chr16p11, VDR_Q3, YY1_01, RASHI_RESPONSE_TO_IONIZING_RADIATION_6, MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP, RAAGNYNNCTTY_UNKNOWN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, PR_Q2, VDR_Q6, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS, PDGF_UP.V1_DN, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_UP

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), 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
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
regulation of DNA-templated transcription	1
transcription regulator activity	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

298 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF688	MRPL43	Q8N983	497
ZNF688	PRR20A	P86496	478
ZNF688	AVL9	Q8NBF6	434
ZNF688	DNTTIP1	Q9H147	416
ZNF688	ZNF618	Q5T7W0	408
ZNF688	HECTD2	Q5U5R9	400
ZNF688	RNPEPL1	Q9HAU8	396
ZNF688	FAM184A	Q8NB25	372
ZNF688	CCDC85C	A6NKD9	371
ZNF688	MOSPD3	O75425	367
ZNF688	ACBD7	Q8N6N7	367
ZNF688	EIF1AY	O14602	356
ZNF688	THAP7	Q9BT49	355
ZNF688	RTP4	Q96DX8	323
ZNF688	PABPC1L	Q4VXU2	306

IntAct

135 interactions, top by confidence:

A	B	Type	Score
SMARCB1	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
TCP11	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
AIRIM	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	HOXA1	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	LMO2	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	FAM90A1	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	RCOR3	psi-mi:“MI:0915”(physical association)	0.560
BOLA2-SMG1P6	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	CCDC102B	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	CIB3	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	PIH1D2	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	ABI2	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	TENT5B	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	PFKFB1	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	CARD9	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	SMARCB1	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	CCNC	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	MKRN3	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	NFU1	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	DEF6	psi-mi:“MI:0915”(physical association)	0.560
PHF1	ZNF688	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	GEM	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	ZNF330	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	MYOZ3	psi-mi:“MI:0915”(physical association)	0.560
ZNF688	GLYCTK	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (120): ZNF688 (Biochemical Activity), TRIM23 (Two-hybrid), CRX (Two-hybrid), GOLGA2 (Two-hybrid), KRT31 (Two-hybrid), REL (Two-hybrid), TRIM27 (Two-hybrid), TCF4 (Two-hybrid), TCF12 (Two-hybrid), TRAF2 (Two-hybrid), CADPS (Two-hybrid), FHL5 (Two-hybrid), GMPPA (Two-hybrid), RINT1 (Two-hybrid), CCDC33 (Two-hybrid)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PPE3, A0A1W2PR82, A0A2Z4LIS9, A2VE02, A4D1S0, A5PKC7, A5PL33, A6H7B4, A6NEL2, A6QP24, A6QPM6, A8MTW9, A8MYA2, D3ZAQ5, D4AAA5, E7EW31, O75474, O75638, O89113, O94850, P0C7X2, P14652, P50617, P70339, Q2KIS6, Q3UN58, Q5JPB2, Q5VZ46, Q6GQX2, Q6NZ36, Q6ZSJ8, Q6ZW13, Q76NI1, Q7TNS8, Q80TS7, Q86UU5, Q8IWN7, Q8N6K4, Q8N944

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Epigenetic regulation of gene expression	5	13.7×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

505 predictions. Top by Δscore:

Variant	Effect	Δscore
16:30570432:ATCTC:A	acceptor_gain	0.9900
16:30570434:CTC:C	acceptor_gain	0.9900
16:30570437:C:CC	acceptor_gain	0.9900
16:30570437:CTGG:C	acceptor_loss	0.9900
16:30570438:T:A	acceptor_loss	0.9900
16:30571044:AGGAT:A	donor_gain	0.9900
16:30571427:CTCT:C	donor_loss	0.9900
16:30571428:TCTCA:T	donor_loss	0.9900
16:30571429:CTCA:C	donor_loss	0.9900
16:30571430:TCA:T	donor_loss	0.9900
16:30571431:CACCG:C	donor_loss	0.9900
16:30571432:ACCGA:A	donor_loss	0.9900
16:30571433:C:A	donor_loss	0.9900
16:30572120:ACC:A	donor_gain	0.9900
16:30572121:CCC:C	donor_gain	0.9900
16:30570435:TC:T	acceptor_gain	0.9800
16:30570436:CC:C	acceptor_gain	0.9800
16:30570446:C:CT	acceptor_gain	0.9800
16:30571426:GCTCT:G	donor_loss	0.9800
16:30571432:A:AC	donor_gain	0.9800
16:30571433:C:CC	donor_gain	0.9800
16:30572121:CCCCT:C	donor_gain	0.9800
16:30572116:ACTTA:A	donor_loss	0.9700
16:30572117:CTTAC:C	donor_loss	0.9700
16:30572118:TTA:T	donor_loss	0.9700
16:30572119:TA:T	donor_loss	0.9700
16:30572120:AC:A	donor_gain	0.9700
16:30572121:CC:C	donor_gain	0.9700
16:30571385:C:A	donor_gain	0.9600
16:30571433:CCGAG:C	donor_gain	0.9600

AlphaMissense

1774 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:30570087:G:C	F220L	1.000
16:30570087:G:T	F220L	1.000
16:30570089:A:G	F220L	1.000
16:30570171:G:C	F192L	1.000
16:30570171:G:T	F192L	1.000
16:30570173:A:G	F192L	1.000
16:30570088:A:G	F220S	0.999
16:30570146:G:C	H201D	0.999
16:30570172:A:G	F192S	0.999
16:30570089:A:T	F220I	0.998
16:30570110:A:G	C213R	0.998
16:30570114:G:C	F211L	0.998
16:30570114:G:T	F211L	0.998
16:30570116:A:G	F211L	0.998
16:30570132:G:C	H205Q	0.998
16:30570132:G:T	H205Q	0.998
16:30570144:G:C	H201Q	0.998
16:30570144:G:T	H201Q	0.998
16:30570146:G:T	H201N	0.998
16:30570172:A:C	F192C	0.998
16:30570173:A:T	F192I	0.998
16:30570194:A:G	C185R	0.998
16:30571510:C:A	W40C	0.998
16:30571510:C:G	W40C	0.998
16:30570060:G:C	H229Q	0.997
16:30570060:G:T	H229Q	0.997
16:30570062:G:C	H229D	0.997
16:30570075:G:C	F224L	0.997
16:30570075:G:T	F224L	0.997
16:30570077:A:G	F224L	0.997

dbSNP variants (sampled 300 via entrez): RS1000122027 (16:30575603 G>A), RS1000431698 (16:30575303 A>G), RS1000780617 (16:30581816 G>A), RS1000922024 (16:30581079 G>A,C), RS1001038511 (16:30573195 C>T), RS1001123878 (16:30574327 C>T), RS1001150489 (16:30575715 G>A), RS1001883987 (16:30575063 G>A,C), RS1002154695 (16:30573590 A>T), RS1002248114 (16:30574117 C>G), RS1002639502 (16:30581750 C>A), RS1002819260 (16:30576918 A>G), RS1003006183 (16:30570127 C>G,T), RS1003108156 (16:30576958 G>T), RS1003567834 (16:30570880 T>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, increases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
sodium arsenate	decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Arsenic	increases abundance, decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Estradiol	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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