ZSCAN5B

Summary

ZSCAN5B (zinc finger and SCAN domain containing 5B, HGNC:34246) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger and SCAN domain-containing protein 5B (A6NJL1). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 342933 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 135 total
• MANE Select transcript: NM_001080456

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34246
Approved symbol	ZSCAN5B
Name	zinc finger and SCAN domain containing 5B
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	ZNF495B, ZNF371
Ensembl gene	ENSG00000197213
Ensembl biotype	protein_coding
OMIM	620918
Entrez	342933

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000586855, ENST00000587032, ENST00000589938

RefSeq mRNA: 2 — MANE Select: NM_001080456 NM_001080456, NM_001385638

CCDS: CCDS46203

Canonical transcript exons

ENST00000586855 — 5 exons

Exon	Start	End
ENSE00002431456	56190837	56190987
ENSE00002517760	56191850	56192053
ENSE00002817005	56197734	56197783
ENSE00002905400	56189686	56190575
ENSE00002963284	56192669	56193179

Expression profiles

Bgee: expression breadth broad, 30 present calls, max score 83.37.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	63.57	gold quality
testis	UBERON:0000473	51.71	gold quality
right testis	UBERON:0004534	50.69	gold quality
left testis	UBERON:0004533	49.59	gold quality
granulocyte	CL:0000094	49.45	silver quality
bone marrow cell	CL:0002092	43.77	gold quality
putamen	UBERON:0001874	43.49	gold quality
prefrontal cortex	UBERON:0000451	42.04	gold quality
sural nerve	UBERON:0015488	41.43	gold quality
islet of Langerhans	UBERON:0000006	40.77	gold quality
ventricular zone	UBERON:0003053	40.53	silver quality
amygdala	UBERON:0001876	40.05	silver quality
temporal lobe	UBERON:0001871	39.92	silver quality
superior frontal gyrus	UBERON:0002661	39.82	silver quality
mucosa of transverse colon	UBERON:0004991	39.53	silver quality
bone marrow	UBERON:0002371	39.39	gold quality
caudate nucleus	UBERON:0001873	38.93	silver quality
frontal cortex	UBERON:0001870	38.87	gold quality
Brodmann (1909) area 9	UBERON:0013540	38.70	silver quality
lower esophagus mucosa	UBERON:0035834	37.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	37.30	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	37.15	silver quality
cerebral cortex	UBERON:0000956	36.91	gold quality
leukocyte	CL:0000738	36.84	silver quality
monocyte	CL:0000576	36.65	silver quality
cortical plate	UBERON:0005343	36.47	gold quality
right lobe of liver	UBERON:0001114	36.09	gold quality
placenta	UBERON:0001987	35.86	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting ZSCAN5B, 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-511-3P	99.99	68.85	1467
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-4490	98.51	68.47	943
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-4800-5P	97.22	65.91	324
HSA-MIR-7847-3P	96.63	64.58	952
HSA-MIR-6760-3P	96.35	68.31	1001
HSA-MIR-3679-5P	94.75	66.46	862
HSA-MIR-1185-5P	94.47	65.95	725

Literature-anchored findings (GeneRIF, showing 2)

• Data implicate the role of ZSCAN5 genes in regulation of Pol III genes and nearby Pol II loci, ultimately influencing cell cycle progression and differentiation in a variety of tissues. (PMID:27732952)
• Using piggyBac transposon gene expression vectors to transfect Zscan5b gene into mouse pluripotent stem cells. (PMID:34541557)

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), ZSCAN5A (ENSG00000131848), 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), ZNF770 (ENSG00000198146), PEG3 (ENSG00000198300), ZSCAN5C (ENSG00000204532)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 5B — A6NJL1 (reviewed: A6NJL1)

All UniProt accessions (3): A6NJL1, K7EJD1, K7ESD3

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

RefSeq proteins (2): NP_001073925, NP_001372567 (=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 (19 total): sequence variant 5, zinc finger region 5, compositionally biased region 4, region of interest 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NJL1-F1	59.70	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FOSTER_KDM1A_TARGETS_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR511_3P, GSE17721_CTRL_VS_PAM3CSK4_12H_BMDC_DN, GSE17721_CTRL_VS_CPG_1H_BMDC_DN, GSE17721_CTRL_VS_GARDIQUIMOD_1H_BMDC_UP, GSE12003_4D_VS_8D_CULTURE_MIR223_KO_BM_PROGENITOR_UP, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, PULVER_FOREY_PERTURB_ATTRITION_M_EG1, GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, chr19q13, GSE3720_UNSTIM_VS_PMA_STIM_VD1_GAMMADELTA_TCELL_DN, GSE4142_NAIVE_VS_MEMORY_BCELL_DN

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), developmental process (GO:0032502)

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

Protein interactions and networks

STRING

272 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN5B	OR2A7	Q96R45	419
ZSCAN5B	METTL26	Q96S19	418
ZSCAN5B	RFPL4A	A6NLU0	393
ZSCAN5B	GAGE2A	Q6NT46	348
ZSCAN5B	RUFY2	Q8WXA3	348
ZSCAN5B	BORCS6	Q96GS4	348
ZSCAN5B	ARGFX	A6NJG6	347
ZSCAN5B	EMC6	Q9BV81	321
ZSCAN5B	GEMIN7	Q9H840	310
ZSCAN5B	KHDC1	Q4VXA5	310
ZSCAN5B	NLRP8	Q86W28	308
ZSCAN5B	RUBCNL	Q9H714	306
ZSCAN5B	TRIM43	Q96BQ3	301
ZSCAN5B	DDX50	Q9BQ39	297
ZSCAN5B	ANO7	Q6IWH7	290
ZSCAN5B	PBLD	P30039	290

IntAct

14 interactions, top by confidence:

A	B	Type	Score
ZSCAN5B	ZBTB7B	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN5B	RINT1	psi-mi:“MI:0915”(physical association)	0.560
	ZSCAN5B	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN5B	PSPC1	psi-mi:“MI:0915”(physical association)	0.560
ZSCAN5B	H1-5	psi-mi:“MI:0915”(physical association)	0.400
ZSCAN5B	ZBTB7B	psi-mi:“MI:0915”(physical association)	0.000
ZSCAN5B	RINT1	psi-mi:“MI:0915”(physical association)	0.000
ZSCAN5B		psi-mi:“MI:0915”(physical association)	0.000
ZSCAN5B	PSPC1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZSCAN5B (Two-hybrid), ZSCAN5B (Two-hybrid), ZSCAN5B (Two-hybrid), HOMEZ (Two-hybrid), HIST1H1B (Proximity Label-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, A2T812, A6NJL1, A6QNZ0, A7KBS4, D2HQI1, O14978, O15535, O43309, O95125, P0CG00, P10073, P17028, P17029, P28698, P49910, Q15697, Q15776, Q16670, Q1LZ87, Q3MJ62, Q3URS2, Q4KLI1, Q4R8H9, Q5R670, Q5RAE6, Q5RJ54, Q5SXI5, Q6NSZ9, Q6R2W3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	119
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

591 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56190572:AGAT:A	acceptor_gain	1.0000
19:56190573:GAT:G	acceptor_gain	1.0000
19:56190575:TC:T	acceptor_loss	1.0000
19:56190576:C:CC	acceptor_gain	1.0000
19:56190577:T:A	acceptor_loss	1.0000
19:56190579:G:GC	acceptor_gain	1.0000
19:56190832:CTCA:C	donor_gain	1.0000
19:56190835:A:AC	donor_gain	1.0000
19:56190836:C:CT	donor_gain	1.0000
19:56190836:CTGGG:C	donor_gain	1.0000
19:56190888:C:A	donor_gain	1.0000
19:56190983:TCTCC:T	acceptor_gain	1.0000
19:56190984:CTCC:C	acceptor_gain	1.0000
19:56190984:CTCCC:C	acceptor_gain	1.0000
19:56190985:TCC:T	acceptor_gain	1.0000
19:56190985:TCCCT:T	acceptor_gain	1.0000
19:56190986:CC:C	acceptor_gain	1.0000
19:56190986:CCC:C	acceptor_gain	1.0000
19:56190987:CC:C	acceptor_gain	1.0000
19:56190988:C:CC	acceptor_gain	1.0000
19:56190988:C:T	acceptor_gain	1.0000
19:56191848:A:AC	donor_gain	1.0000
19:56191848:A:AT	donor_loss	1.0000
19:56191849:C:CA	donor_gain	1.0000
19:56191849:CCTG:C	donor_gain	1.0000
19:56192049:ATAGA:A	acceptor_gain	1.0000
19:56192050:TAGA:T	acceptor_gain	1.0000
19:56192051:AGA:A	acceptor_gain	1.0000
19:56192052:GA:G	acceptor_gain	1.0000
19:56192054:C:CC	acceptor_gain	1.0000

AlphaMissense

3269 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56189971:G:C	F448L	1.000
19:56189971:G:T	F448L	1.000
19:56189973:A:G	F448L	1.000
19:56190055:G:C	F420L	1.000
19:56190055:G:T	F420L	1.000
19:56190057:A:G	F420L	1.000
19:56189887:G:C	F476L	0.999
19:56189887:G:T	F476L	0.999
19:56189889:A:G	F476L	0.999
19:56189910:A:G	C469R	0.999
19:56189932:G:C	H461Q	0.999
19:56189932:G:T	H461Q	0.999
19:56189939:C:G	R459P	0.999
19:56189954:A:G	L454P	0.999
19:56189972:A:G	F448S	0.999
19:56189994:A:G	C441R	0.999
19:56190056:A:G	F420S	0.999
19:56190069:A:G	C416R	0.999
19:56190078:A:G	C413R	0.999
19:56190139:G:C	F392L	0.999
19:56190139:G:T	F392L	0.999
19:56190141:A:G	F392L	0.999
19:56190223:A:C	F364L	0.999
19:56190223:A:T	F364L	0.999
19:56190225:A:G	F364L	0.999
19:56190246:A:G	C357R	0.999
19:56189860:G:C	H485Q	0.998
19:56189860:G:T	H485Q	0.998
19:56189888:A:G	F476S	0.998
19:56189916:A:C	Y467D	0.998

dbSNP variants (sampled 300 via entrez): RS1000060764 (19:56196734 G>C), RS1000289615 (19:56191904 C>A,T), RS1001129675 (19:56195501 G>A), RS1001317775 (19:56191396 T>C), RS1001385753 (19:56192485 T>C), RS1001417030 (19:56192242 A>G), RS1001446304 (19:56195850 T>A), RS1001497669 (19:56195643 G>A), RS1001602298 (19:56191559 A>C,T), RS1001708609 (19:56196832 A>G), RS1002309865 (19:56195696 G>C,T), RS1002419720 (19:56191221 G>A), RS1002644353 (19:56195957 C>G), RS1002724512 (19:56192404 T>A), RS1002977643 (19:56197890 T>C)

Disease associations

OMIM: gene MIM:620918 | 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases mutagenesis	2
Malathion	decreases expression	1
Tobacco Smoke Pollution	decreases methylation	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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