ZCCHC13

Summary

ZCCHC13 (zinc finger CCHC-type containing 13, HGNC:31749) is a protein-coding gene on chromosome Xq13.2, encoding Zinc finger CCHC domain-containing protein 13 (Q8WW36).

This gene appears to represent an intronless retrocopy of a related multi-exon gene located on chromosome 3. However, the CDS of this intronless gene remains relatively intact, it is conserved in other mammalian species, it is known to be transcribed, and it is therefore thought to encode a functional protein. The encoded protein contains six CCHC-type zinc fingers, and is thus thought to function as a transcription factor.

Source: NCBI Gene 389874 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_203303

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31749
Approved symbol	ZCCHC13
Name	zinc finger CCHC-type containing 13
Location	Xq13.2
Locus type	gene with protein product
Status	Approved
Aliases	4930513O09RIK, Cnbp2, ZNF9L
Ensembl gene	ENSG00000187969
Ensembl biotype	protein_coding
OMIM	301125
Entrez	389874

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000339534

RefSeq mRNA: 1 — MANE Select: NM_203303 NM_203303

CCDS: CCDS14425

Canonical transcript exons

ENST00000339534 — 1 exons

Exon	Start	End
ENSE00001374013	74304180	74305034

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 84.34.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0335 / max 31.1249, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196756	0.0192	3
196755	0.0143	3

Top tissues by expression

232 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	84.34	gold quality
left testis	UBERON:0004533	83.33	gold quality
right testis	UBERON:0004534	81.17	gold quality
testis	UBERON:0000473	80.25	gold quality
buccal mucosa cell	CL:0002336	59.77	silver quality
tendon of biceps brachii	UBERON:0008188	48.11	gold quality
adult organism	UBERON:0007023	46.78	gold quality
deltoid	UBERON:0001476	45.91	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	42.42	gold quality
quadriceps femoris	UBERON:0001377	42.35	gold quality
biceps brachii	UBERON:0001507	42.15	gold quality
colonic epithelium	UBERON:0000397	41.77	gold quality
inferior vagus X ganglion	UBERON:0005363	41.49	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
oviduct epithelium	UBERON:0004804	41.21	gold quality
trigeminal ganglion	UBERON:0001675	41.14	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
epithelium of nasopharynx	UBERON:0001951	40.45	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality
esophagus squamous epithelium	UBERON:0006920	40.29	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	40.27	gold quality
jejunum	UBERON:0002115	40.18	gold quality
cartilage tissue	UBERON:0002418	40.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting ZCCHC13, 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-5193	100.00	67.26	1744
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-302B-5P	99.50	69.49	1857
HSA-MIR-302D-5P	99.50	69.34	1863
HSA-MIR-7109-5P	99.18	66.13	1057
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-6749-3P	99.00	65.73	1443
HSA-MIR-6877-3P	98.98	65.83	560
HSA-MIR-6819-3P	98.95	65.57	572
HSA-MIR-3124-3P	98.87	68.95	2123
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-6887-5P	98.56	68.49	1295
HSA-MIR-6795-5P	98.52	68.51	1277
HSA-MIR-4691-5P	98.41	66.77	1343
HSA-MIR-6792-3P	98.41	66.86	1359

Literature-anchored findings (GeneRIF, showing 1)

• ZCCHC13 functions an oncogene for hepatocellular carcinoma, and DNA hypomethylation is a driving factor in carcinogenesis. (PMID:30940166)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	cnbpa	ENSDARG00000045776
danio_rerio	cnbpb	ENSDARG00000070922
mus_musculus	Zcchc13	ENSMUSG00000031330
rattus_norvegicus	Zcchc13	ENSRNOG00000002923
drosophila_melanogaster	CNBP	FBGN0034802
caenorhabditis_elegans		WBGENE00019537

Paralogs (3): ZCCHC9 (ENSG00000131732), ZCCHC7 (ENSG00000147905), CNBP (ENSG00000169714)

Protein

Protein identifiers

Zinc finger CCHC domain-containing protein 13 — Q8WW36 (reviewed: Q8WW36)

All UniProt accessions (1): Q8WW36

RefSeq proteins (1): NP_976048* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001878	Znf_CCHC	Domain
IPR036875	Znf_CCHC_sf	Homologous_superfamily

Pfam: PF00098

UniProt features (7 total): zinc finger region 6, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WW36-F1	66.67	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSLATION_REGULATOR_ACTIVITY, GOBP_REGULATION_OF_CYTOPLASMIC_TRANSLATION, GOBP_POSITIVE_REGULATION_OF_TRANSLATION, GOBP_REGULATION_OF_TRANSLATION, TAATTA_CHX10_01, GOBP_POSITIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOMF_MRNA_BINDING, GOMF_SINGLE_STRANDED_RNA_BINDING, GOBP_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, MIKKELSEN_ES_ICP_WITH_H3K4ME3, chrXq13, GOBP_POSITIVE_REGULATION_OF_CYTOPLASMIC_TRANSLATION

GO Biological Process (1): positive regulation of cytoplasmic translation (GO:2000767)

GO Molecular Function (7): single-stranded RNA binding (GO:0003727), mRNA binding (GO:0003729), zinc ion binding (GO:0008270), translation regulator activity (GO:0045182), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA binding	2
binding	2
cytoplasmic translation	1
positive regulation of translation	1
regulation of cytoplasmic translation	1
transition metal ion binding	1
molecular_function	1
regulation of translation	1
cation binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1150 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZCCHC13	DMPK	Q09013	581
ZCCHC13	CHIC1	Q5VXU3	519
ZCCHC13	MBNL1	Q9NR56	495
ZCCHC13	MBNL2	Q5VZF2	434
ZCCHC13	MBNL3	Q9NUK0	433
ZCCHC13	FAM47B	Q8NA70	411
ZCCHC13	NME2	P22392	409
ZCCHC13	HNRNPK	P61978	408
ZCCHC13	SATL1	Q86VE3	402
ZCCHC13	ZCCHC9	Q8N567	397
ZCCHC13	RLIM	Q9NVW2	396
ZCCHC13	LARP1B	Q659C4	387
ZCCHC13	SLC16A2	P36021	380
ZCCHC13	NUCLEOLIN	P19338	360
ZCCHC13	CLCN1	P35523	348

IntAct

17 interactions, top by confidence:

A	B	Type	Score
SIAH1	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.560
ZCCHC13	SIAH1	psi-mi:“MI:0915”(physical association)	0.560
ZNF648	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.560
SNRPA	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.560
ZNF250	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.560
ZCCHC13	GUCD1	psi-mi:“MI:0915”(physical association)	0.560
ZNF648	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.000
GUCD1	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.000
SNRPA	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.000
ZNF250	ZCCHC13	psi-mi:“MI:0915”(physical association)	0.000
ZCCHC13	ATXN1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): ZCCHC13 (Two-hybrid), ZCCHC13 (Two-hybrid), ZCCHC13 (Two-hybrid), ZCCHC13 (Two-hybrid), ZNF250 (Two-hybrid), ZCCHC13 (Two-hybrid)

ESM2 similar proteins: A8WLV5, E0X9N4, O42395, O65639, P09052, P24346, P34689, P36627, P53849, P53996, P62633, P62634, P91599, P92186, Q04832, Q09476, Q0JD07, Q18034, Q3MSQ8, Q3T0Q6, Q4JG17, Q4R5S7, Q54NW4, Q5NU13, Q5R5R5, Q5W5U4, Q5ZA07, Q61496, Q64060, Q67YE6, Q6GWX0, Q6IDS6, Q7F8R0, Q7XPK1, Q84MZ4, Q8T8R1, Q8VZ42, Q8WW36, Q91372, Q94C69

Diamond homologs: O42395, P53996, P62633, P62634, Q3T0Q6, Q5R5R5, Q8RWN5, Q8WW36

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	2
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

260 predictions. Top by Δscore:

Variant	Effect	Δscore
X:74304402:A:AG	acceptor_gain	0.9100
X:74304455:C:A	acceptor_gain	0.9000
X:74304274:G:GG	donor_gain	0.8800
X:74304456:G:A	acceptor_gain	0.8700
X:74304271:GCA:G	donor_gain	0.8600
X:74304462:ATCT:A	acceptor_gain	0.8000
X:74304416:T:TA	acceptor_gain	0.7800
X:74304463:T:G	acceptor_gain	0.7800
X:74304462:A:AG	acceptor_gain	0.7500
X:74304403:C:G	acceptor_gain	0.7400
X:74304269:GAGCA:G	donor_gain	0.7200
X:74304371:TTCTC:T	donor_gain	0.7200
X:74304400:A:AG	acceptor_gain	0.7200
X:74304465:T:TA	acceptor_gain	0.7200
X:74304411:T:A	acceptor_gain	0.6800
X:74304401:C:G	acceptor_gain	0.6700
X:74304402:ACCT:A	acceptor_gain	0.6700
X:74304505:G:GG	donor_gain	0.6700
X:74304353:TGG:T	donor_gain	0.6600
X:74304354:G:GA	donor_gain	0.6600
X:74304405:T:TA	acceptor_gain	0.6400
X:74304510:GATCC:G	donor_gain	0.6400
X:74304415:GTG:G	donor_gain	0.6300
X:74304414:T:A	acceptor_gain	0.5900
X:74304754:G:GT	donor_gain	0.5900
X:74304755:A:T	donor_gain	0.5900
X:74304279:G:GT	donor_gain	0.5800
X:74304381:G:GA	donor_gain	0.5800
X:74304501:GACT:G	donor_gain	0.5800
X:74304476:T:TA	acceptor_gain	0.5700

AlphaMissense

1074 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:74304626:C:A	H120Q	0.761
X:74304626:C:G	H120Q	0.761
X:74304563:T:A	H99Q	0.732
X:74304563:T:G	H99Q	0.732
X:74304635:A:C	K123N	0.715
X:74304635:A:T	K123N	0.715
X:74304680:C:A	H138Q	0.693
X:74304680:C:G	H138Q	0.693
X:74304685:C:A	A140D	0.683
X:74304634:A:T	K123I	0.678
X:74304632:G:C	Q122H	0.676
X:74304632:G:T	Q122H	0.676
X:74304491:C:A	H75Q	0.659
X:74304491:C:G	H75Q	0.659
X:74304653:G:C	K129N	0.639
X:74304653:G:T	K129N	0.639
X:74304657:T:G	Y131D	0.636
X:74304500:A:C	K78N	0.627
X:74304500:A:T	K78N	0.627
X:74304600:T:A	C112S	0.627
X:74304601:G:C	C112S	0.627
X:74304561:C:G	H99D	0.624
X:74304609:T:A	C115S	0.615
X:74304610:G:C	C115S	0.615
X:74304613:G:T	G116V	0.611
X:74304654:T:A	C130S	0.611
X:74304655:G:C	C130S	0.611
X:74304539:T:G	C91W	0.609
X:74304496:C:A	A77D	0.599
X:74304667:G:T	G134V	0.589

dbSNP variants (sampled 300 via entrez): RS1001564499 (X:74304357 G>A,C), RS1002266041 (X:74304903 T>C), RS1002298592 (X:74305465 G>A), RS1004406889 (X:74303979 A>C), RS1007231326 (X:74303420 G>C), RS1007283764 (X:74302969 T>C), RS1011123525 (X:74302772 C>A), RS1013344269 (X:74302366 A>C), RS1013375357 (X:74302766 G>A,T), RS1015176551 (X:74303088 A>G), RS1015928630 (X:74304967 C>T), RS1017354062 (X:74303035 A>G), RS1019322308 (X:74303586 A>C), RS1026543666 (X:74304180 A>T), RS1026687578 (X:74302428 A>G)

Disease associations

OMIM: gene MIM:301125 | 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

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
clothianidin	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Rifampin	decreases expression	1

Clinical trials (associated diseases)

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