ZSCAN5C

Summary

ZSCAN5C (zinc finger and SCAN domain containing 5C, HGNC:34294) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger and SCAN domain-containing protein 5C (A6NGD5). 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 649137 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001358413

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34294
Approved symbol	ZSCAN5C
Name	zinc finger and SCAN domain containing 5C
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	ZNF495C
Ensembl gene	ENSG00000204532
Ensembl biotype	protein_coding
Entrez	649137

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000534327

RefSeq mRNA: 1 — MANE Select: NM_001358413 NM_001358413

CCDS: CCDS86811

Canonical transcript exons

ENST00000534327 — 5 exons

Exon	Start	End
ENSE00001469997	56208034	56208184
ENSE00002155741	56202273	56202322
ENSE00002495044	56205787	56206297
ENSE00002525187	56207059	56207262
ENSE00003978191	56208449	56209461

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 77.48.

Top tissues by expression

123 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	77.48	silver quality
stromal cell of endometrium	CL:0002255	39.44	gold quality
granulocyte	CL:0000094	39.10	gold quality
mucosa of transverse colon	UBERON:0004991	38.63	silver quality
bone marrow cell	CL:0002092	38.17	gold quality
ganglionic eminence	UBERON:0004023	37.31	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
skeletal muscle tissue	UBERON:0001134	36.54	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow	UBERON:0002371	35.06	gold quality
mucosa of stomach	UBERON:0001199	34.92	gold quality
gall bladder	UBERON:0002110	33.86	gold quality
muscle tissue	UBERON:0002385	33.38	gold quality
right lung	UBERON:0002167	32.90	gold quality
duodenum	UBERON:0002114	32.61	gold quality
vermiform appendix	UBERON:0001154	32.20	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
prefrontal cortex	UBERON:0000451	31.79	gold quality
urinary bladder	UBERON:0001255	31.76	gold quality
leukocyte	CL:0000738	31.01	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
tonsil	UBERON:0002372	30.48	gold quality
right uterine tube	UBERON:0001302	30.37	gold quality
primary visual cortex	UBERON:0002436	30.27	gold quality
lymph node	UBERON:0000029	30.07	gold quality
blood	UBERON:0000178	29.52	gold quality
monocyte	CL:0000576	29.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	29.03	gold quality
heart left ventricle	UBERON:0002084	28.77	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.45

Regulation

Is transcription factor: no

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), ZSCAN5B (ENSG00000197213), ZNF770 (ENSG00000198146), PEG3 (ENSG00000198300)

Protein

Protein identifiers

Zinc finger and SCAN domain-containing protein 5C — A6NGD5 (reviewed: A6NGD5)

Alternative names: Zinc finger and SCAN domain-containing protein 5C pseudogene

All UniProt accessions (1): A6NGD5

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_001345342* (*=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): compositionally biased region 5, zinc finger region 5, sequence variant 4, region of interest 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NGD5-F1	60.08	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, TBPL1_TARGET_GENES, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, chr19q13

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

GO Molecular Function (4): 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), 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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

146 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSCAN5C	UBTFL1	P0CB47	372
ZSCAN5C	METTL26	Q96S19	354
ZSCAN5C	BORCS6	Q96GS4	273
ZSCAN5C	GEMIN7	Q9H840	253
ZSCAN5C	POLR3E	Q9NVU0	226
ZSCAN5C	TRIM7	Q9C029	216
ZSCAN5C	POLR3A	O14802	182
ZSCAN5C	MAF1	Q9H063	178
ZSCAN5C	ALOXE3	Q9BYJ1	177
ZSCAN5C	HTN1	P15515	161
ZSCAN5C	STAP2	Q9UGK3	161
ZSCAN5C	GTF3C1	Q12789	159
ZSCAN5C	BDP1	A6H8Y1	155
ZSCAN5C	SSBP1	Q04837	143
ZSCAN5C	EXOC6	Q8TAG9	136

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A1YEW3, A1YG31, A2T715, A2T7M0, A6NEV1, A6NGD5, A6NJL1, A6QPT6, A8MXV6, A8MZF0, A8WFF7, O08664, P03327, P06936, P0C6A0, P0DPQ3, P54257, P57086, P86478, P86479, P86480, P86481, P86496, Q13487, Q32PG5, Q505G4, Q5R7P6, Q68FX5, Q6J1H4, Q6NZN1, Q6ZMS7, Q6ZRT6, Q76NI1, Q7L3V2, Q7TPK6, Q7YR42, Q7Z6I6, Q80UE6, Q8IY33, Q8K2W9

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YEW3, A1YFW2, A1YG26, A1YG31, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T712, A2T715, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T7M0, A2T812, A6NGD5, A6NJL1, A6QNZ0, A6QPT6, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P0CG00, P10073, P17028, P17029, P28698, P49910

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

556 predictions. Top by Δscore:

Variant	Effect	Δscore
19:56205785:A:AG	acceptor_gain	1.0000
19:56205785:AG:A	acceptor_loss	1.0000
19:56205786:G:GA	acceptor_loss	1.0000
19:56205786:G:GG	acceptor_gain	1.0000
19:56206294:ATGGG:A	donor_loss	1.0000
19:56206295:TGG:T	donor_gain	1.0000
19:56206295:TGGGT:T	donor_loss	1.0000
19:56206296:GGG:G	donor_gain	1.0000
19:56206298:G:GG	donor_gain	1.0000
19:56208026:A:AG	acceptor_gain	1.0000
19:56208027:T:G	acceptor_gain	1.0000
19:56208029:CTCAG:C	acceptor_loss	1.0000
19:56208033:G:GT	acceptor_gain	1.0000
19:56208033:GGA:G	acceptor_gain	1.0000
19:56208033:GGAA:G	acceptor_gain	1.0000
19:56208180:TCCCA:T	donor_gain	1.0000
19:56208185:G:GG	donor_gain	1.0000
19:56208189:G:GG	donor_gain	1.0000
19:56202319:GGAG:G	donor_gain	0.9900
19:56202320:GAGG:G	donor_gain	0.9900
19:56202320:GAGGT:G	donor_loss	0.9900
19:56202323:GTAA:G	donor_loss	0.9900
19:56205594:G:T	donor_gain	0.9900
19:56205786:GA:G	acceptor_gain	0.9900
19:56205786:GAC:G	acceptor_gain	0.9900
19:56205786:GACT:G	acceptor_gain	0.9900
19:56205786:GACTT:G	acceptor_gain	0.9900
19:56206293:AATGG:A	donor_gain	0.9900
19:56206294:ATGG:A	donor_gain	0.9900
19:56206296:GG:G	donor_gain	0.9900

AlphaMissense

3277 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:56209054:T:C	F449L	1.000
19:56209056:C:A	F449L	1.000
19:56209056:C:G	F449L	1.000
19:56208958:T:C	C417R	0.999
19:56208970:T:C	F421L	0.999
19:56208971:T:C	F421S	0.999
19:56208972:C:A	F421L	0.999
19:56208972:C:G	F421L	0.999
19:56208997:C:G	H430D	0.999
19:56209055:T:C	F449S	0.999
19:56208802:T:C	F365L	0.998
19:56208804:T:A	F365L	0.998
19:56208804:T:G	F365L	0.998
19:56208843:C:A	H378Q	0.998
19:56208843:C:G	H378Q	0.998
19:56208886:T:C	F393L	0.998
19:56208888:C:A	F393L	0.998
19:56208888:C:G	F393L	0.998
19:56208920:G:C	R404P	0.998
19:56208949:T:C	C414R	0.998
19:56208960:C:G	C417W	0.998
19:56209011:C:A	H434Q	0.998
19:56209011:C:G	H434Q	0.998
19:56209027:T:C	F440L	0.998
19:56209029:C:A	F440L	0.998
19:56209029:C:G	F440L	0.998
19:56209033:T:C	C442R	0.998
19:56209073:T:C	L455P	0.998
19:56209088:G:C	R460P	0.998
19:56209138:T:C	F477L	0.998

dbSNP variants (sampled 300 via entrez): RS1000012947 (19:56203783 G>A), RS1000338027 (19:56201193 A>C), RS1000396033 (19:56206362 T>C), RS1000407421 (19:56206508 A>C,T), RS1000512616 (19:56209658 T>C), RS1000543622 (19:56209365 A>G,T), RS1000672024 (19:56201414 G>A), RS1001543940 (19:56208945 C>A,T), RS1001837952 (19:56201074 TTTTG>T), RS1001915333 (19:56205893 T>A,C), RS1002001843 (19:56201255 A>G), RS1002073944 (19:56200949 A>G), RS1002521137 (19:56207635 G>A,C), RS1002543741 (19:56207629 T>C), RS1002667576 (19:56203607 A>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

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

Chemical	Actions (top 5)	PubMed papers
potassium chromate(VI)	increases expression	1
K 7174	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Catechin	decreases expression, affects cotreatment	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW95	HEK293 eGFP-ZSCAN5C	Transformed cell line	Female

Clinical trials (associated diseases)

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