ZCCHC10

Summary

ZCCHC10 (zinc finger CCHC-type containing 10, HGNC:25954) is a protein-coding gene on chromosome 5q31.1, encoding Zinc finger CCHC domain-containing protein 10 (Q8TBK6).

Predicted to enable nucleic acid binding activity and zinc ion binding activity.

Source: NCBI Gene 54819 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_001300816

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25954
Approved symbol	ZCCHC10
Name	zinc finger CCHC-type containing 10
Location	5q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20094
Ensembl gene	ENSG00000155329
Ensembl biotype	protein_coding
Entrez	54819

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000324170, ENST00000355372, ENST00000504170, ENST00000506403, ENST00000508080, ENST00000509008, ENST00000509437, ENST00000511440, ENST00000513541, ENST00000513848, ENST00000877908, ENST00000877909, ENST00000877910, ENST00000877911, ENST00000877912, ENST00000928631, ENST00000928632, ENST00000928633, ENST00000971357

RefSeq mRNA: 10 — MANE Select: NM_001300816 NM_001300816, NM_001300817, NM_001300818, NM_001300819, NM_001300822, NM_001308127, NM_001308128, NM_001308129, NM_001308130, NM_017665

CCDS: CCDS4165, CCDS75300, CCDS75301, CCDS75302, CCDS78059, CCDS78060

Canonical transcript exons

ENST00000509437 — 5 exons

Exon	Start	End
ENSE00001430540	133022841	133022906
ENSE00001811879	132996985	132998850
ENSE00003497848	133006759	133006920
ENSE00003622853	133026497	133026549
ENSE00003640392	133000132	133000173

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 95.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.3074 / max 357.8567, expressed in 1805 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63386	22.3074	1805

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	95.23	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.27	gold quality
amniotic fluid	UBERON:0000173	91.73	gold quality
mucosa of transverse colon	UBERON:0004991	91.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.27	gold quality
palpebral conjunctiva	UBERON:0001812	91.21	gold quality
epithelium of nasopharynx	UBERON:0001951	89.91	gold quality
parietal pleura	UBERON:0002400	89.86	gold quality
esophagus squamous epithelium	UBERON:0006920	89.77	gold quality
monocyte	CL:0000576	89.70	gold quality
rectum	UBERON:0001052	89.62	gold quality
oocyte	CL:0000023	89.53	gold quality
mononuclear cell	CL:0000842	89.49	gold quality
germinal epithelium of ovary	UBERON:0001304	89.47	gold quality
leukocyte	CL:0000738	89.37	gold quality
visceral pleura	UBERON:0002401	89.26	gold quality
pleura	UBERON:0000977	88.98	gold quality
buccal mucosa cell	CL:0002336	88.88	gold quality
islet of Langerhans	UBERON:0000006	88.38	gold quality
lower esophagus mucosa	UBERON:0035834	88.12	gold quality
esophagus mucosa	UBERON:0002469	88.05	gold quality
endometrium	UBERON:0001295	87.94	gold quality
gastrocnemius	UBERON:0001388	87.88	gold quality
muscle of leg	UBERON:0001383	87.70	gold quality
cortical plate	UBERON:0005343	87.45	gold quality
ganglionic eminence	UBERON:0004023	87.27	gold quality
vermiform appendix	UBERON:0001154	87.24	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	87.24	gold quality
transverse colon	UBERON:0001157	87.20	gold quality
lymph node	UBERON:0000029	87.09	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.88
E-MTAB-7303	no	182.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

104 targeting ZCCHC10, 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-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867

Literature-anchored findings (GeneRIF, showing 1)

• ZCCHC10 exerts its tumor-suppressive effects by stabilizing the p53 protein and can be used a potential prognostic marker and therapeutic target in lung adenocarcinoma. (PMID:31138778)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	zcchc10	ENSDARG00000091092
mus_musculus	Zcchc10	ENSMUSG00000018239
rattus_norvegicus	AABR07072108.1	ENSRNOG00000006943
drosophila_melanogaster	CG5516	FBGN0038389

Protein

Protein identifiers

Zinc finger CCHC domain-containing protein 10 — Q8TBK6 (reviewed: Q8TBK6)

All UniProt accessions (6): Q8TBK6, B3KVL5, D6R9G7, D6RHC2, D6RIV3, G3XAM1

Isoforms (2)

UniProt ID	Names	Canonical?
Q8TBK6-1	1	yes
Q8TBK6-2	2

RefSeq proteins (10): NP_001287745, NP_001287746, NP_001287747, NP_001287748, NP_001287751, NP_001295056, NP_001295057, NP_001295058, NP_001295059, NP_060135 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR036875	Znf_CCHC_sf	Homologous_superfamily
IPR039715	ZCCHC10	Family

Pfam: PF13917

UniProt features (6 total): compositionally biased region 2, chain 1, zinc finger region 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TBK6-F1	64.31	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): GARY_CD5_TARGETS_DN, LYF1_01, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN, chr5q31, CHEN_HOXA5_TARGETS_9HR_UP, WGTTNNNNNAAA_UNKNOWN, WILCOX_RESPONSE_TO_PROGESTERONE_UP, COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP, PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN, WHITFIELD_CELL_CYCLE_M_G1, JOHNSTONE_PARVB_TARGETS_3_DN, LEE_BMP2_TARGETS_DN, RATTENBACHER_BOUND_BY_CELF1, ESC_J1_UP_LATE.V1_DN, ESC_V6.5_UP_LATE.V1_DN

GO Biological Process (0):

GO Molecular Function (4): nucleic acid binding (GO:0003676), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
transition metal ion binding	1
cation binding	1

Protein interactions and networks

STRING

1546 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZCCHC10	PITX1	P78337	570
ZCCHC10	THAP1	Q9NVV9	482
ZCCHC10	HCFC1	P51610	454
ZCCHC10	PHF1	O43189	449
ZCCHC10	U2AF2	P26368	419
ZCCHC10	DVL2	O14641	412
ZCCHC10	STRBP	Q96SI9	407
ZCCHC10	C5orf24	Q7Z6I8	391
ZCCHC10	FXR2	P51116	372
ZCCHC10	ANKRD13C	Q8N6S4	367
ZCCHC10	YJU2B	P13994	352
ZCCHC10	A0A0A6YYJ8	A0A0A6YYJ8	350
ZCCHC10	LUC7L2	Q9Y383	348
ZCCHC10	TTC14	Q96N46	335
ZCCHC10	ZNF117	Q03924	325

IntAct

178 interactions, top by confidence:

A	B	Type	Score
THAP1	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.790
ZCCHC10	THAP1	psi-mi:“MI:0915”(physical association)	0.790
ZCCHC10	PSME3	psi-mi:“MI:0915”(physical association)	0.780
STAC3	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.780
PSME3	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.780
ZCCHC10	STAC3	psi-mi:“MI:0915”(physical association)	0.780
ZCCHC10	DZIP3	psi-mi:“MI:0915”(physical association)	0.740
DZIP3	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.740
ZCCHC10	MCRS1	psi-mi:“MI:0915”(physical association)	0.740
MED19	MED19	psi-mi:“MI:0914”(association)	0.730
SFMBT1	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.720
ZCCHC10	SFMBT1	psi-mi:“MI:0915”(physical association)	0.720
TFCP2	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.670
RBM39	ZCCHC10	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (270): ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid), ZCCHC10 (Two-hybrid)

ESM2 similar proteins: A0JNI5, A2AJT4, A2AQ19, D3ZTQ1, O00193, P35269, P97762, Q02614, Q0IIX4, Q12872, Q2T9Y0, Q3THK3, Q3USH5, Q4QQU1, Q53F19, Q5EA53, Q5EB97, Q5HZB6, Q5PPJ2, Q5RAD5, Q5U2T8, Q5U3K5, Q5XG50, Q5ZHP7, Q5ZI03, Q5ZK28, Q6AXS3, Q6AY96, Q6DDU5, Q7TN31, Q7TNC4, Q811X5, Q86X95, Q8CFC7, Q8N2M8, Q8R149, Q8TBK6, Q8TF01, Q91ZD6, Q92541

Diamond homologs: Q5EB97, Q8TBK6, Q9CX48

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
mRNA Splicing - Major Pathway	16	19.0×	2e-14
mRNA Polyadenylation	8	15.3×	7e-06
mRNA Splicing	6	14.3×	3e-04
Processing of Capped Intron-Containing Pre-mRNA	7	12.5×	1e-04
Dengue Virus-Host Interactions	8	7.9×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	15	21.5×	9e-14
RNA splicing	10	13.8×	5e-07
mRNA processing	7	8.6×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

726 predictions. Top by Δscore:

Variant	Effect	Δscore
5:133000182:C:CT	acceptor_gain	1.0000
5:133000184:C:CT	acceptor_gain	1.0000
5:133000185:G:T	acceptor_gain	1.0000
5:133006754:CCTA:C	donor_loss	1.0000
5:133006755:CTACC:C	donor_loss	1.0000
5:133006756:TACC:T	donor_loss	1.0000
5:133006757:ACCT:A	donor_loss	1.0000
5:133006758:C:A	donor_loss	1.0000
5:133006916:CTTCA:C	acceptor_gain	1.0000
5:133006917:TTCA:T	acceptor_gain	1.0000
5:133006918:TCA:T	acceptor_gain	1.0000
5:133006919:CA:C	acceptor_gain	1.0000
5:133006919:CAC:C	acceptor_gain	1.0000
5:133006920:AC:A	acceptor_loss	1.0000
5:133006921:C:CC	acceptor_gain	1.0000
5:133006921:CTA:C	acceptor_loss	1.0000
5:133006924:C:CT	acceptor_gain	1.0000
5:133026491:A:AC	donor_gain	1.0000
5:133026492:C:CC	donor_gain	1.0000
5:133026492:CTTA:C	donor_gain	1.0000
5:133026495:A:AC	donor_gain	1.0000
5:133026495:ACG:A	donor_gain	1.0000
5:133026496:C:CC	donor_gain	1.0000
5:133026496:CG:C	donor_gain	1.0000
5:133026496:CGC:C	donor_gain	1.0000
5:133026496:CGCTT:C	donor_gain	1.0000
5:132998849:ACC:A	acceptor_loss	0.9900
5:132998852:T:G	acceptor_loss	0.9900
5:133000174:C:CC	acceptor_gain	0.9900
5:133006752:AACCT:A	donor_loss	0.9900

AlphaMissense

1267 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:133006827:C:A	R67S	1.000
5:133006827:C:G	R67S	1.000
5:133006828:C:A	R67M	1.000
5:133006828:C:G	R67T	1.000
5:133006842:T:A	R62S	1.000
5:133006842:T:G	R62S	1.000
5:133006854:G:C	C58W	1.000
5:133006855:C:A	C58F	1.000
5:133006855:C:G	C58S	1.000
5:133006855:C:T	C58Y	1.000
5:133006856:A:G	C58R	1.000
5:133006856:A:T	C58S	1.000
5:133006866:C:A	W54C	1.000
5:133006866:C:G	W54C	1.000
5:133006868:A:G	W54R	1.000
5:133006868:A:T	W54R	1.000
5:133006871:G:C	H53D	1.000
5:133006873:C:T	G52E	1.000
5:133006885:C:G	C48S	1.000
5:133006886:A:G	C48R	1.000
5:133006886:A:T	C48S	1.000
5:133006890:C:A	Q46H	1.000
5:133006890:C:G	Q46H	1.000
5:133006894:C:G	C45S	1.000
5:133006895:A:G	C45R	1.000
5:133006895:A:T	C45S	1.000
5:133006807:A:G	L74P	0.999
5:133006818:C:A	R70S	0.999
5:133006818:C:G	R70S	0.999
5:133006819:C:A	R70M	0.999

dbSNP variants (sampled 300 via entrez): RS1000072463 (5:133010699 G>A), RS1000123952 (5:132998180 TAACA>T), RS1000278132 (5:133007409 G>A), RS1000372793 (5:133004652 C>A,T), RS1000441185 (5:133000855 C>G,T), RS1000443058 (5:133013891 T>C), RS1000538351 (5:133028476 G>A,T), RS1000606503 (5:133027192 A>G), RS1000765840 (5:133000000 G>T), RS1000913534 (5:133023436 C>T), RS1000989550 (5:133016996 C>T), RS1001045553 (5:133023264 C>A,G,T), RS1001116787 (5:133012486 T>C,G), RS1001139900 (5:133023114 C>T), RS1001243831 (5:132997049 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

1 associations (top):

Study	Trait	p-value
GCST003476_5	Eyebrow thickness	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, decreases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	decreases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
sodium arsenite	increases abundance, increases expression, affects cotreatment	1
cobaltous chloride	increases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
cylindrospermopsin	increases expression	1
jinfukang	decreases expression	1
Vorinostat	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Coumestrol	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Gold	decreases expression	1
Hydrogen Peroxide	affects cotreatment, decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	increases expression	1
Ozone	affects expression, increases abundance	1
Progesterone	increases expression	1
Smoke	decreases expression	1
Theophylline	decreases expression, affects cotreatment	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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