ZSCAN29

Summary

ZSCAN29 (zinc finger and SCAN domain containing 29, HGNC:26673) is a protein-coding gene on chromosome 15q15.3, encoding Zinc finger and SCAN domain-containing protein 29 (Q8IWY8). May be involved in transcriptional regulation.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 146050 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 133 total
• MANE Select transcript: NM_001372080

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26673
Approved symbol	ZSCAN29
Name	zinc finger and SCAN domain containing 29
Location	15q15.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35867, Zfp690
Ensembl gene	ENSG00000140265
Ensembl biotype	protein_coding
OMIM	620932
Entrez	146050

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000396976, ENST00000562072, ENST00000563508, ENST00000566849, ENST00000568898, ENST00000570181, ENST00000684362, ENST00000923737, ENST00000942834, ENST00000942835

RefSeq mRNA: 2 — MANE Select: NM_001372080 NM_001372080, NM_152455

CCDS: CCDS10095

Canonical transcript exons

ENST00000684362 — 6 exons

Exon	Start	End
ENSE00001046091	43363915	43364382
ENSE00001227942	43366110	43366808
ENSE00002593969	43369596	43370025
ENSE00002605100	43370558	43371043
ENSE00003720306	43368923	43369127
ENSE00003920328	43358175	43361941

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 97.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2481 / max 59.4992, expressed in 1684 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149606	5.2481	1684

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.18	gold quality
tendon of biceps brachii	UBERON:0008188	95.24	gold quality
oocyte	CL:0000023	91.41	gold quality
pancreatic ductal cell	CL:0002079	90.12	gold quality
medial globus pallidus	UBERON:0002477	89.99	gold quality
cerebellar vermis	UBERON:0004720	89.57	gold quality
epithelium of nasopharynx	UBERON:0001951	88.92	gold quality
globus pallidus	UBERON:0001875	88.72	gold quality
cardia of stomach	UBERON:0001162	88.54	gold quality
thymus	UBERON:0002370	88.32	gold quality
right testis	UBERON:0004534	87.81	gold quality
left testis	UBERON:0004533	87.71	gold quality
inferior vagus X ganglion	UBERON:0005363	87.65	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.59	gold quality
pylorus	UBERON:0001166	87.33	gold quality
pericardium	UBERON:0002407	86.68	gold quality
tendon	UBERON:0000043	86.53	gold quality
testis	UBERON:0000473	86.51	gold quality
ganglionic eminence	UBERON:0004023	85.89	gold quality
ventricular zone	UBERON:0003053	85.81	gold quality
lower lobe of lung	UBERON:0008949	85.56	gold quality
mucosa of paranasal sinus	UBERON:0005030	85.28	gold quality
subthalamic nucleus	UBERON:0001906	85.21	gold quality
nasal cavity epithelium	UBERON:0005384	85.18	gold quality
endometrium	UBERON:0001295	84.71	gold quality
medulla oblongata	UBERON:0001896	84.67	gold quality
ventral tegmental area	UBERON:0002691	84.54	gold quality
renal medulla	UBERON:0000362	84.31	gold quality
oviduct epithelium	UBERON:0004804	84.26	gold quality
monocyte	CL:0000576	83.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.96

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1602.1	ZSCAN29	More than 3 adjacent zinc fingers
MA1602.2	ZSCAN29	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28473536

miRNA regulators (miRDB)

116 targeting ZSCAN29, 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-340-5P	100.00	72.50	4437
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-544A	99.84	68.66	1965
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6885-3P	99.75	70.36	3187

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	plagx	ENSDARG00000036855
danio_rerio	ovol1a	ENSDARG00000076472
danio_rerio	plagl2	ENSDARG00000076657
danio_rerio	ovol1b	ENSDARG00000078256
mus_musculus	Zscan29	ENSMUSG00000050619
drosophila_melanogaster	hb	FBGN0001180
drosophila_melanogaster	CG12391	FBGN0033581
caenorhabditis_elegans		WBGENE00001824
caenorhabditis_elegans		WBGENE00003033
caenorhabditis_elegans		WBGENE00012385

Paralogs (29): ZNF446 (ENSG00000083838), REST (ENSG00000084093), ZNF174 (ENSG00000103343), OVOL3 (ENSG00000105261), PLAGL1 (ENSG00000118495), ZSCAN18 (ENSG00000121413), ZNF576 (ENSG00000124444), OVOL2 (ENSG00000125850), PLAGL2 (ENSG00000126003), ZSCAN5A (ENSG00000131848), ZSCAN32 (ENSG00000140987), ZSCAN1 (ENSG00000152467), ZNF18 (ENSG00000154957), ZKSCAN2 (ENSG00000155592), ZNF496 (ENSG00000162714), ZNF202 (ENSG00000166261), ZNF641 (ENSG00000167528), ZNF444 (ENSG00000167685), SCAND1 (ENSG00000171222), ZNF274 (ENSG00000171606), ZNF131 (ENSG00000172262), OVOL1 (ENSG00000172818), ZNF518A (ENSG00000177853), ZNF518B (ENSG00000178163), PLAG1 (ENSG00000181690), ZSCAN5B (ENSG00000197213), ZNF770 (ENSG00000198146), PEG3 (ENSG00000198300), ZSCAN5C (ENSG00000204532)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 29 — Q8IWY8 (reviewed: Q8IWY8)

Alternative names: Zinc finger protein 690

All UniProt accessions (5): Q8IWY8, A0A0C4DGM2, C9K0J8, H3BMU4, H3BUW4

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 (4)

UniProt ID	Names	Canonical?
Q8IWY8-1	1	yes
Q8IWY8-2	2
Q8IWY8-3	3
Q8IWY8-4	4

RefSeq proteins (2): NP_001359009, NP_689668 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily
IPR044822	Myb_DNA-bind_4	Domain

Pfam: PF00096, PF02023, PF13837

UniProt features (27 total): zinc finger region 6, region of interest 4, cross-link 4, splice variant 4, compositionally biased region 2, modified residue 2, sequence variant 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWY8-F1	54.05	0.02

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6): 153, 561, 112, 180, 576, 652

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 86 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, CREL_01, SCGGAAGY_ELK1_02, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ELK1_02, HORIUCHI_WTAP_TARGETS_UP, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, NRF1_Q6, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GLI3_TARGET_GENES, HES4_TARGET_GENES, HHEX_TARGET_GENES

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): 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), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), sequence-specific DNA binding (GO:0043565), 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	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	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
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

980 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN29	KNDC1	Q76NI1	518
ZSCAN29	ARMCX4	Q5H9R4	480
ZSCAN29	SLF2	Q8IX21	430
ZSCAN29	M9MMK7	M9MMK7	418
ZSCAN29	CDCP2	Q5VXM1	417
ZSCAN29	PDAP1	Q13442	408
ZSCAN29	ENOPH1	Q9UHY7	400
ZSCAN29	PCMTD1	Q96MG8	399
ZSCAN29	KCTD6	Q8NC69	396
ZSCAN29	MOCOS	Q96EN8	390
ZSCAN29	MED11	Q9P086	381
ZSCAN29	IGSF10	Q6WRI0	380
ZSCAN29	PHETA2	Q6ICB4	380
ZSCAN29	VENTX	O95231	370
ZSCAN29	NUDT5	Q9UKK9	370
ZSCAN29	PCDHGB4	Q9UN71	370

IntAct

12 interactions, top by confidence:

A	B	Type	Score
ZSCAN32	ZNF197	psi-mi:“MI:0914”(association)	0.530
ZSCAN29	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
NS1	ESYT2	psi-mi:“MI:0914”(association)	0.350
NS1	SAC3D1	psi-mi:“MI:0914”(association)	0.350
MAD2L1	MED19	psi-mi:“MI:0914”(association)	0.350
ZNF232	ZNF197	psi-mi:“MI:0914”(association)	0.350
ZSCAN20	ZNF197	psi-mi:“MI:0914”(association)	0.350
ZSCAN23	ZNF263	psi-mi:“MI:0914”(association)	0.350
ZSCAN29	GSDME	psi-mi:“MI:0914”(association)	0.350
ZSCAN29	ACTB	psi-mi:“MI:0914”(association)	0.350
	TTC8	psi-mi:“MI:0914”(association)	0.350

BioGRID (39): ZSCAN29 (Affinity Capture-RNA), ZSCAN29 (Affinity Capture-RNA), ZSCAN29 (Affinity Capture-MS), ZSCAN29 (Affinity Capture-MS), ZSCAN29 (Affinity Capture-MS), ZSCAN29 (Affinity Capture-MS), ZSCAN29 (Affinity Capture-MS), RPGRIP1L (Affinity Capture-MS), EHD2 (Affinity Capture-MS), LRP2 (Affinity Capture-MS), MAD2L1BP (Affinity Capture-MS), DFNA5 (Affinity Capture-MS), ABAT (Affinity Capture-MS), ZSCAN29 (Affinity Capture-MS), ZSCAN29 (Two-hybrid)

ESM2 similar proteins: A0A0J9YX57, A1A5P9, A2A368, A2A9R3, A8MXT2, B2KFW1, O15479, O15480, O15481, O15553, P0C6Y7, P10073, P17040, P25233, P43355, P43356, P43357, P43358, P43360, P43362, P43363, P43364, P43366, Q13342, Q16666, Q4R998, Q5PPP4, Q5RD14, Q6AY37, Q6PCZ4, Q8BQR7, Q8IWY8, Q8IX06, Q8N660, Q8N7X4, Q8TD90, Q96DU7, Q96LZ2, Q96M61, Q99608

Diamond homologs: A0A1W2PQ72, B2KFW1, P17040, Q63HK3, Q8IWY8, Q9NX65, A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	113
Likely benign	10
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

935 predictions. Top by Δscore:

Variant	Effect	Δscore
15:43363973:AGTAT:A	donor_gain	1.0000
15:43361941:CC:C	acceptor_loss	0.9900
15:43361941:CCTGA:C	acceptor_gain	0.9900
15:43361942:CTGAT:C	acceptor_loss	0.9900
15:43361943:T:G	acceptor_loss	0.9900
15:43361945:A:C	acceptor_gain	0.9900
15:43363908:ATCTT:A	donor_loss	0.9900
15:43363912:TACCA:T	donor_loss	0.9900
15:43363914:C:T	donor_loss	0.9900
15:43363914:CCA:C	donor_gain	0.9900
15:43364001:T:TA	donor_gain	0.9900
15:43364390:C:CT	acceptor_gain	0.9900
15:43366813:T:C	acceptor_gain	0.9900
15:43366813:T:TC	acceptor_gain	0.9900
15:43368874:TCCCA:T	donor_gain	0.9900
15:43368875:C:A	donor_gain	0.9900
15:43368901:C:A	donor_gain	0.9900
15:43368922:CCG:C	donor_gain	0.9900
15:43369586:C:CA	donor_gain	0.9900
15:43369590:TCTCA:T	donor_loss	0.9900
15:43369591:CTCAC:C	donor_loss	0.9900
15:43369592:TCA:T	donor_loss	0.9900
15:43369593:CAC:C	donor_loss	0.9900
15:43369595:C:CA	donor_loss	0.9900
15:43369611:T:TA	donor_gain	0.9900
15:43361887:T:TA	donor_gain	0.9800
15:43361942:C:CC	acceptor_gain	0.9800
15:43361945:A:AC	acceptor_gain	0.9800
15:43363913:A:AC	donor_gain	0.9800
15:43363914:C:CC	donor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000117155 (15:43360479 T>C), RS1000237121 (15:43360819 C>A,T), RS1000882208 (15:43360972 C>G), RS1001353317 (15:43367882 C>T), RS1001561541 (15:43371101 A>C,G), RS1001628627 (15:43371651 G>T), RS1001689482 (15:43371123 G>C,T), RS1001898643 (15:43362283 G>A), RS1001966352 (15:43370298 C>A), RS1002177383 (15:43359136 C>T), RS1002262930 (15:43372200 T>A,C), RS1002510765 (15:43369291 C>A), RS1002520984 (15:43364974 T>C), RS1002695494 (15:43372574 C>T), RS1002739641 (15:43372917 G>A)

Disease associations

OMIM: gene MIM:620932 | 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

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, increases abundance, increases expression, increases oxidation, affects expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Ozone	increases oxidation, increases abundance, affects expression, affects cotreatment, increases expression	2
Valproic Acid	affects expression, decreases methylation	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases abundance, affects cotreatment, increases expression, increases oxidation	1
bisphenol A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
methacrylaldehyde	affects cotreatment, increases expression, increases oxidation, increases abundance	1
avobenzone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Acrolein	increases oxidation, increases abundance, affects cotreatment, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Cadmium	increases abundance, increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Phenobarbital	affects expression	1
Testosterone	decreases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1
Urethane	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Gold Compounds	decreases expression	1
Cadmium Chloride	increases abundance, increases 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_XW94	HEK293 eGFP-ZSCAN29	Transformed cell line	Female

Clinical trials (associated diseases)

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