ZSCAN5A

Summary

ZSCAN5A (zinc finger and SCAN domain containing 5A, HGNC:23710) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger and SCAN domain-containing protein 5A (Q9BUG6). 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 79149 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 106 total
• MANE Select transcript: NM_001322064

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23710
Approved symbol	ZSCAN5A
Name	zinc finger and SCAN domain containing 5A
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	MGC4161
Ensembl gene	ENSG00000131848
Ensembl biotype	protein_coding
OMIM	620916
Entrez	79149

Gene structure

Transcript identifiers

Ensembl transcripts: 37 — 29 protein_coding, 7 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000391713, ENST00000585670, ENST00000586031, ENST00000587075, ENST00000587340, ENST00000587492, ENST00000587614, ENST00000588442, ENST00000588955, ENST00000589279, ENST00000590675, ENST00000591078, ENST00000592101, ENST00000592355, ENST00000592509, ENST00000592679, ENST00000593106, ENST00000683990, ENST00000891612, ENST00000891613, ENST00000891614, ENST00000891615, ENST00000891616, ENST00000891617, ENST00000891618, ENST00000928141, ENST00000928142, ENST00000928143, ENST00000928144, ENST00000928145, ENST00000948522, ENST00000948523, ENST00000948524, ENST00000948525, ENST00000948526, ENST00000948527, ENST00000948528

RefSeq mRNA: 23 — MANE Select: NM_001322064 NM_001322061, NM_001322062, NM_001322064, NM_001322065, NM_001322066, NM_001322067, NM_001322068, NM_001322070, NM_001322072, NM_001322073, NM_001322074, NM_001322075, NM_001322076, NM_001322077, NM_001322078, NM_001387853, NM_001387854, NM_001387855, NM_001387856, NM_001387857, NM_001387858, NM_001387859, NM_024303

CCDS: CCDS12941, CCDS82403

Canonical transcript exons

ENST00000683990 — 6 exons

Exon	Start	End
ENSE00002443833	56224663	56225173
ENSE00002488128	56222591	56222741
ENSE00002966521	56314681	56314839
ENSE00003539074	56223631	56223834
ENSE00003690801	56313283	56313384
ENSE00003921797	56221303	56222326

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 89.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.8159 / max 54.1666, expressed in 1750 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182877	5.5964	1750
182876	0.0839	23
182874	0.0633	20
182875	0.0517	21
182873	0.0206	12

Top tissues by expression

276 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	89.69	gold quality
right testis	UBERON:0004534	89.19	gold quality
sperm	CL:0000019	88.55	silver quality
left testis	UBERON:0004533	88.19	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.63	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.62	gold quality
testis	UBERON:0000473	86.40	gold quality
apex of heart	UBERON:0002098	86.24	gold quality
male germ cell	CL:0000015	86.23	silver quality
right uterine tube	UBERON:0001302	85.94	gold quality
right atrium auricular region	UBERON:0006631	84.65	gold quality
heart left ventricle	UBERON:0002084	83.39	gold quality
cardiac ventricle	UBERON:0002082	82.70	gold quality
cardiac atrium	UBERON:0002081	82.07	gold quality
gastrocnemius	UBERON:0001388	81.98	gold quality
nucleus accumbens	UBERON:0001882	81.77	gold quality
muscle of leg	UBERON:0001383	81.76	gold quality
adenohypophysis	UBERON:0002196	81.38	gold quality
heart	UBERON:0000948	80.92	gold quality
caudate nucleus	UBERON:0001873	80.41	gold quality
monocyte	CL:0000576	80.39	gold quality
prefrontal cortex	UBERON:0000451	80.27	gold quality
mononuclear cell	CL:0000842	80.22	gold quality
leukocyte	CL:0000738	80.12	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	80.09	gold quality
right ovary	UBERON:0002118	79.93	gold quality
putamen	UBERON:0001874	79.89	gold quality
right lobe of thyroid gland	UBERON:0001119	79.74	gold quality
left ovary	UBERON:0002119	79.31	gold quality
pituitary gland	UBERON:0000007	79.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting ZSCAN5A, 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-570-3P	99.96	72.41	4910
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-3129-3P	97.85	67.63	1246
HSA-MIR-5583-5P	97.85	67.61	1243
HSA-MIR-592	96.59	67.59	817

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	plagx	ENSDARG00000036855
danio_rerio	ovol1a	ENSDARG00000076472
danio_rerio	plagl2	ENSDARG00000076657
danio_rerio	ovol1b	ENSDARG00000078256
mus_musculus	Zscan5b	ENSMUSG00000058028
rattus_norvegicus	Zscan5b	ENSRNOG00000049014
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), ZSCAN29 (ENSG00000140265), 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 5A — Q9BUG6 (reviewed: Q9BUG6)

Alternative names: Zinc finger protein 495

All UniProt accessions (8): A0A0C4DGQ1, Q9BUG6, K7EIX9, K7EMC4, K7EN85, K7EQW6, K7ESE4, K7ESN6

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BUG6-1	1	yes
Q9BUG6-2	2

RefSeq proteins (23): NP_001308990, NP_001308991, NP_001308993, NP_001308994, NP_001308995, NP_001308996, NP_001308997, NP_001308999, NP_001309001, NP_001309002, NP_001309003, NP_001309004, NP_001309005, NP_001309006, NP_001309007, NP_001374782, NP_001374783, NP_001374784, NP_001374785, NP_001374786, NP_001374787, NP_001374788, NP_077279 (=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
IPR050331	Zinc_finger_PRDM4/PRDM1/PRDM14	Family

Pfam: PF00096, PF02023, PF12874

UniProt features (20 total): zinc finger region 5, compositionally biased region 3, sequence conflict 3, splice variant 2, sequence variant 2, region of interest 2, chain 1, domain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BUG6-F1	58.50	0.14

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 (1): 159

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, WHITFIELD_CELL_CYCLE_M_G1, ZWANG_EGF_INTERVAL_UP, NOTCH_DN.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CEBPZ_TARGET_GENES, DLX6_TARGET_GENES, ELF2_TARGET_GENES, NAB2_TARGET_GENES, ZFP91_TARGET_GENES, ZNF33A_TARGET_GENES, ZNF528_TARGET_GENES, ZNF592_TARGET_GENES, ZSCAN2_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), protein binding (GO:0005515), 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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

494 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN5A	EOLA2	Q96DE9	540
ZSCAN5A	KHDC1	Q4VXA5	433
ZSCAN5A	TRIM43	Q96BQ3	405
ZSCAN5A	HHIPL2	Q6UWX4	379
ZSCAN5A	RFPL4A	A6NLU0	371
ZSCAN5A	PRAMEF10	O60809	356
ZSCAN5A	DMRTB1	Q96MA1	331
ZSCAN5A	GPR45	Q9Y5Y3	322
ZSCAN5A	RUFY2	Q8WXA3	314
ZSCAN5A	C21orf91	Q9NYK6	312
ZSCAN5A	CCSAP	Q6IQ19	311
ZSCAN5A	MGAT4C	Q9UBM8	311
ZSCAN5A	MALRD1	Q5VYJ5	310
ZSCAN5A	PRAMEF11	O60813	302
ZSCAN5A	HMGN3	Q15651	297

IntAct

19 interactions, top by confidence:

A	B	Type	Score
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
NFU1	ZSCAN5A	psi-mi:“MI:0915”(physical association)	0.560
CIB3	ZSCAN5A	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN5A	NFU1	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	ZSCAN5A	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN5A	KDM1A	psi-mi:“MI:0914”(association)	0.530
ZMYM4	ILVBL	psi-mi:“MI:0914”(association)	0.530
	ZSCAN5A	psi-mi:“MI:0915”(physical association)	0.400
ZSCAN5A	MRPS12	psi-mi:“MI:0914”(association)	0.350
ZSCAN5A	HDAC3	psi-mi:“MI:0914”(association)	0.350
ZSCAN5A	GAPDHS	psi-mi:“MI:0914”(association)	0.350
ZMYM2	ZBTB5	psi-mi:“MI:2364”(proximity)	0.270
ZSCAN5A	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (60): EPHB4 (Affinity Capture-MS), HMGA1 (Affinity Capture-MS), MRPS12 (Affinity Capture-MS), ZMYM2 (Affinity Capture-MS), ZMYM4 (Affinity Capture-MS), IPO8 (Affinity Capture-MS), ZNF616 (Affinity Capture-MS), CDYL2 (Affinity Capture-MS), RCOR2 (Affinity Capture-MS), IPO8 (Affinity Capture-MS), ZMYM2 (Affinity Capture-MS), CSNK2A2 (Affinity Capture-MS), SCAND1 (Affinity Capture-MS), RCOR3 (Affinity Capture-MS), CSNK2A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D5NS60, A0JN76, A1YFX5, A2T7G6, A6NJL1, D2HQI1, F1MJR8, O14901, P0CG00, P10754, P22227, P98182, Q0IJ29, Q1L8W0, Q3SWU4, Q5DW34, Q5EAC5, Q5EXX3, Q5RHB5, Q5SXI5, Q5T619, Q66H04, Q6NRM8, Q6NV66, Q6ZSB9, Q7M6U3, Q7TS63, Q7TSH3, Q7ZWZ4, Q801P1, Q86VK4, Q8BKX7, Q8BXX2, Q8NAM6, Q8NAP3, Q8NCP5, Q8R0A2, Q91VW9, Q96IT1, Q96N77

Diamond homologs: A1YEP8, A1YFW2, A1YFX5, A1YG60, A1YGJ4, A2T6E3, A2T6V8, A2T736, A2T7D7, A2T7F4, A2T7G6, A6QNZ0, A7KBS4, D2HQI1, O14978, O15535, O43309, O60304, P0CG00, P10073, P17028, P49910, Q15697, Q15776, Q16670, Q1LZ87, Q3MJ62, Q3URS2, Q4R8H9, Q5RAE6, Q5RJ54, Q5SXI5, Q6NSZ9, Q6R2W3, Q80VJ6, Q86W11, Q8BGS3, Q8CF60, Q8IWY8, Q8N0Y2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	90
Likely benign	10
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2212 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56222324:CTG:C	acceptor_gain	1.0000
19:56222327:C:CC	acceptor_gain	1.0000
19:56222586:CTCA:C	donor_gain	1.0000
19:56222589:A:AC	donor_gain	1.0000
19:56222590:C:CT	donor_gain	1.0000
19:56222590:CTGGG:C	donor_gain	1.0000
19:56222642:C:A	donor_gain	1.0000
19:56222737:TCTCC:T	acceptor_gain	1.0000
19:56222738:CTCC:C	acceptor_gain	1.0000
19:56222738:CTCCC:C	acceptor_gain	1.0000
19:56222739:TCC:T	acceptor_gain	1.0000
19:56222739:TCCC:T	acceptor_loss	1.0000
19:56222739:TCCCT:T	acceptor_gain	1.0000
19:56222740:CC:C	acceptor_gain	1.0000
19:56222740:CCC:C	acceptor_gain	1.0000
19:56222741:CC:C	acceptor_gain	1.0000
19:56222742:C:CC	acceptor_gain	1.0000
19:56222742:C:T	acceptor_gain	1.0000
19:56223629:A:AC	donor_gain	1.0000
19:56223629:ACCTG:A	donor_gain	1.0000
19:56223630:C:CG	donor_loss	1.0000
19:56223630:C:CT	donor_gain	1.0000
19:56223630:CCTG:C	donor_gain	1.0000
19:56223630:CCTGC:C	donor_gain	1.0000
19:56223830:ACAGA:A	acceptor_gain	1.0000
19:56223831:CAGA:C	acceptor_gain	1.0000
19:56223831:CAGAC:C	acceptor_gain	1.0000
19:56223832:AGA:A	acceptor_gain	1.0000
19:56223833:GA:G	acceptor_gain	1.0000
19:56223834:ACTG:A	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000019743 (19:56302105 A>C), RS1000031411 (19:56253687 G>A), RS1000046315 (19:56259761 T>C), RS1000055361 (19:56255462 C>T), RS1000059660 (19:56337355 G>A), RS1000077553 (19:56260029 A>G), RS1000087570 (19:56298044 G>A), RS1000132283 (19:56245640 G>A,C,T), RS1000160610 (19:56296174 G>A), RS1000163622 (19:56258642 C>A), RS1000187378 (19:56225677 A>C), RS1000207621 (19:56240152 ACT>A), RS1000253258 (19:56331524 T>C), RS1000256183 (19:56265313 A>G), RS1000258949 (19:56258317 G>A)

Disease associations

OMIM: gene MIM:620916 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST003253_2	Microalbuminuria	5.000000e-06
GCST006464_11	Endometrial cancer	3.000000e-07
GCST90002393_675	Monocyte count	1.000000e-12
GCST90002394_569	Monocyte percentage of white cells	6.000000e-12

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005091	monocyte count
EFO:0007989	monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	2
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
geraniol	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
benzo(e)pyrene	increases methylation	1
ferrous chloride	decreases expression	1
aflatoxin B2	increases methylation	1
CGP 52608	affects binding, increases reaction	1
ICG 001	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Carbamazepine	affects expression	1
Cisplatin	affects cotreatment, decreases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Methapyrilene	increases methylation	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Zinc	affects cotreatment, increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A8L2	SEES3-1V human ZSCAN5A, clone1	Embryonic stem cell	Male
CVCL_A8L3	SEES3-1V human ZSCAN5A, clone2	Embryonic stem cell	Male
CVCL_A8L4	SEES3-1V human ZSCAN5A, clone3	Embryonic stem cell	Male
CVCL_HD50	HEK293 eGFP-ZSCAN5A	Transformed cell line	Female

Clinical trials (associated diseases)

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