ZNF729

Summary

ZNF729 (zinc finger protein 729, HGNC:32464) is a protein-coding gene on chromosome 19p12, encoding Zinc finger protein 729 (A6NN14). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 100287226 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 215 total
• MANE Select transcript: NM_001242680

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32464
Approved symbol	ZNF729
Name	zinc finger protein 729
Location	19p12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000196350
Ensembl biotype	protein_coding
Entrez	100287226

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000601693

RefSeq mRNA: 1 — MANE Select: NM_001242680 NM_001242680

CCDS: CCDS59368

Canonical transcript exons

ENST00000601693 — 4 exons

Exon	Start	End
ENSE00002382526	22303758	22303884
ENSE00002397682	22304688	22304783
ENSE00003019750	22313671	22317176
ENSE00003172719	22286441	22286555

Expression profiles

Bgee: expression breadth tissue_specific, 8 present calls, max score 82.71.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3323 / max 231.4305, expressed in 28 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
174902	0.2631	25
174901	0.0692	13

Top tissues by expression

128 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	82.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.94	gold quality
ventricular zone	UBERON:0003053	54.02	silver quality
testis	UBERON:0000473	49.06	gold quality
ganglionic eminence	UBERON:0004023	48.97	gold quality
right testis	UBERON:0004534	45.88	gold quality
left testis	UBERON:0004533	45.73	gold quality
endometrium	UBERON:0001295	41.39	silver quality
vermiform appendix	UBERON:0001154	40.54	gold quality
placenta	UBERON:0001987	40.29	gold quality
stromal cell of endometrium	CL:0002255	38.68	gold quality
sural nerve	UBERON:0015488	38.00	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
superior frontal gyrus	UBERON:0002661	36.26	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
primary visual cortex	UBERON:0002436	35.54	gold quality
prefrontal cortex	UBERON:0000451	35.13	gold quality
urinary bladder	UBERON:0001255	34.76	gold quality
monocyte	CL:0000576	34.27	gold quality
islet of Langerhans	UBERON:0000006	33.88	gold quality
leukocyte	CL:0000738	33.67	gold quality
lymph node	UBERON:0000029	33.45	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
muscle tissue	UBERON:0002385	33.33	gold quality
smooth muscle tissue	UBERON:0001135	33.00	gold quality
bone marrow	UBERON:0002371	32.78	gold quality
duodenum	UBERON:0002114	32.57	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
frontal cortex	UBERON:0001870	31.41	gold quality
gall bladder	UBERON:0002110	30.84	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-10018	yes	317.83
E-ANND-3	yes	2.94
E-MTAB-7249	no	2.45

Regulation

Is transcription factor: no

Cross-species orthologs

30 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
drosophila_melanogaster	Sry-delta	FBGN0003512
drosophila_melanogaster	az2	FBGN0025185
drosophila_melanogaster	hang	FBGN0026575
drosophila_melanogaster	CG3032	FBGN0029928
drosophila_melanogaster	CG2129	FBGN0030008
drosophila_melanogaster	CG11695	FBGN0030316
drosophila_melanogaster	CG8944	FBGN0030680
drosophila_melanogaster	CG7101	FBGN0030963
drosophila_melanogaster	CG1602	FBGN0033186
drosophila_melanogaster	CG18011	FBGN0033491
drosophila_melanogaster	CG12942	FBGN0033569
drosophila_melanogaster	CG8089	FBGN0033993
drosophila_melanogaster	indra	FBGN0035213
drosophila_melanogaster	CG10654	FBGN0036294
drosophila_melanogaster	CG6791	FBGN0037918
drosophila_melanogaster	CG17803	FBGN0038547
drosophila_melanogaster	CG12219	FBGN0043796
drosophila_melanogaster	CG30020	FBGN0050020
drosophila_melanogaster	pzg	FBGN0259785
drosophila_melanogaster	mld	FBGN0263490
drosophila_melanogaster	zf30C	FBGN0270924
caenorhabditis_elegans	ztf-15	WBGENE00011066
caenorhabditis_elegans		WBGENE00013734
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), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), 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 729 — A6NN14 (reviewed: A6NN14)

All UniProt accessions (1): A6NN14

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 (1): NP_001229609* (*=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
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096, PF01352, PF13912

UniProt features (39 total): zinc finger region 37, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NN14-F1	69.48	0.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 17 (showing top): chr19p12, CUI_TCF21_TARGETS_2_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HMGA1_TARGET_GENES, GSE8685_IL15_ACT_IL2_STARVED_VS_IL21_ACT_IL2_STARVED_CD4_TCELL_DN, GSE7596_AKT_TRANSD_VS_CTRL_CD4_TCONV_WITH_TGFB_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOBP_NEGATIVE_REGULATION_OF_RNA_BIOSYNTHETIC_PROCESS, GSE2770_IL12_VS_IL4_TREATED_ACT_CD4_TCELL_2H_UP, REACTOME_RNA_POLYMERASE_II_TRANSCRIPTION

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (4): DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
regulation of transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
negative regulation of transcription by RNA polymerase II	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
nucleic acid binding	1
transition metal ion 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
ZNF729	BOD1L2	Q8IYS8	452
ZNF729	FAM47C	Q5HY64	395
ZNF729	CCDC167	Q9P0B6	370
ZNF729	TRIM60	Q495X7	368
ZNF729	LRTM3	Q8NDH2	348
ZNF729	ACTRT3	Q9BYD9	314
ZNF729	OGFRL1	Q5TC84	305
ZNF729	ANKRD36C	Q5JPF3	305
ZNF729	VMA22	Q96NT0	301
ZNF729	TMEM187	Q14656	301
ZNF729	MZT1	Q08AG7	283
ZNF729	TMEM14A	Q9Y6G1	270
ZNF729	GOLT1A	Q6ZVE7	270
ZNF729	B4E1Z4	B4E1Z4	270
ZNF729	KHDC3L	Q587J8	265

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ECE1	ZNF729	psi-mi:“MI:0915”(physical association)	0.370
ZNF729	PPM1G	psi-mi:“MI:0914”(association)	0.350
RNF10	ZNF729	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): ZNF729 (Affinity Capture-MS), ZNF729 (Cross-Linking-MS (XL-MS)), ZNF729 (Co-fractionation), ZNF729 (Co-fractionation), ZNF729 (Co-fractionation)

ESM2 similar proteins: A2VDQ7, A6NK75, A6NN14, A6NNF4, A8MQ14, A8MTY0, A8MXY4, B7Z6K7, E9QAG8, O43345, O75290, O75373, O75437, P0CJ79, P10751, P17017, P17019, P17035, P17038, P18749, P35789, P51522, Q03923, Q03938, Q05481, Q14585, Q3SYV7, Q4V348, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6P5C7, Q6ZN08, Q6ZN57, Q6ZR52, Q86V71, Q86XN6, Q8IYB9, Q8N7Q3

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	197
Likely benign	12
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

690 predictions. Top by Δscore:

Variant	Effect	Δscore
19:22303752:TTTCA:T	acceptor_loss	1.0000
19:22303753:TTCAG:T	acceptor_loss	1.0000
19:22303754:TCAG:T	acceptor_loss	1.0000
19:22303755:CA:C	acceptor_loss	1.0000
19:22303845:G:T	donor_gain	1.0000
19:22303880:CCTGG:C	donor_loss	1.0000
19:22303881:CTGGG:C	donor_loss	1.0000
19:22303882:TGGG:T	donor_loss	1.0000
19:22303883:GG:G	donor_gain	1.0000
19:22303884:GG:G	donor_gain	1.0000
19:22303884:GGTGA:G	donor_loss	1.0000
19:22303885:GTG:G	donor_loss	1.0000
19:22303886:T:G	donor_loss	1.0000
19:22286556:GTGAG:G	donor_loss	0.9900
19:22303756:A:AG	acceptor_gain	0.9900
19:22303756:AG:A	acceptor_gain	0.9900
19:22303756:AGG:A	acceptor_gain	0.9900
19:22303757:G:GG	acceptor_gain	0.9900
19:22303757:GG:G	acceptor_gain	0.9900
19:22303757:GGG:G	acceptor_gain	0.9900
19:22303757:GGGAC:G	acceptor_gain	0.9900
19:22303885:G:GG	donor_gain	0.9900
19:22303887:G:GC	donor_loss	0.9900
19:22303890:GA:G	donor_gain	0.9900
19:22313669:A:AG	acceptor_gain	0.9900
19:22313670:G:GG	acceptor_gain	0.9900
19:22313670:GTT:G	acceptor_gain	0.9900
19:22313670:GTTA:G	acceptor_gain	0.9900
19:22313670:GTTAT:G	acceptor_gain	0.9900
19:22286521:C:G	donor_gain	0.9800

AlphaMissense

8394 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:22316334:T:C	F973L	0.975
19:22316336:T:A	F973L	0.975
19:22316336:T:G	F973L	0.975
19:22314654:T:C	F413L	0.974
19:22314656:T:A	F413L	0.974
19:22314656:T:G	F413L	0.974
19:22314738:T:C	F441L	0.973
19:22314740:T:A	F441L	0.973
19:22314740:T:G	F441L	0.973
19:22314990:T:C	F525L	0.970
19:22314992:T:A	F525L	0.970
19:22314992:T:G	F525L	0.970
19:22315410:T:C	F665L	0.969
19:22315412:T:A	F665L	0.969
19:22315412:T:G	F665L	0.969
19:22315578:T:C	F721L	0.967
19:22315580:T:A	F721L	0.967
19:22315580:T:G	F721L	0.967
19:22315326:T:C	F637L	0.966
19:22315328:T:A	F637L	0.966
19:22315328:T:G	F637L	0.966
19:22315074:T:C	F553L	0.965
19:22315076:T:A	F553L	0.965
19:22315076:T:G	F553L	0.965
19:22315494:T:C	F693L	0.964
19:22315496:T:A	F693L	0.964
19:22315496:T:G	F693L	0.964
19:22315998:T:C	F861L	0.959
19:22316000:T:A	F861L	0.959
19:22316000:T:G	F861L	0.959

dbSNP variants (sampled 300 via entrez): RS1000216820 (19:22285131 CTG>C), RS1000308977 (19:22295545 C>G,T), RS1000319415 (19:22290293 G>A), RS1000410167 (19:22316820 G>A), RS1000757145 (19:22293914 A>G), RS1000821410 (19:22295089 TTG>T), RS1000882900 (19:22299323 A>G), RS1000915281 (19:22298921 T>C), RS1001271492 (19:22293579 G>A,T), RS1001314381 (19:22297967 C>T), RS1001403283 (19:22295792 T>C), RS1001430699 (19:22304042 T>TTC), RS1001510778 (19:22305330 T>C), RS1001571615 (19:22309843 G>A), RS1001602543 (19:22309499 C>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

3 associations (top):

Study	Trait	p-value
GCST005312_13	Menopause (age at onset)	4.000000e-08
GCST010599_13	Dietary fat liking	5.000000e-06
GCST010599_7	Dietary fat liking	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004704	age at menopause
EFO:0010816	dietary fat liking measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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