ZC3H11C

Summary

ZC3H11C (zinc finger CCCH-type containing 11C, HGNC:56304) is a protein-coding gene on chromosome 6q12, encoding Zinc finger CCCH domain-containing protein 11C (P0DQW0).

Predicted to enable zinc ion binding activity. Predicted to be involved in poly(A)+ mRNA export from nucleus.

Source: NCBI Gene 441155 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total — 1 pathogenic
• MANE Select transcript: NM_001271675

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:56304
Approved symbol	ZC3H11C
Name	zinc finger CCCH-type containing 11C
Location	6q12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000214558
Ensembl biotype	protein_coding
Entrez	441155

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000398578

RefSeq mRNA: 1 — MANE Select: NM_001271675 NM_001271675

CCDS: CCDS93939

Canonical transcript exons

ENST00000398578 — 2 exons

Exon	Start	End
ENSE00002371359	65302021	65306574
ENSE00003970576	65301476	65301650

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 63.62.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
testis	UBERON:0000473	63.62	gold quality
left testis	UBERON:0004533	63.41	gold quality
right testis	UBERON:0004534	62.85	gold quality
sural nerve	UBERON:0015488	41.00	gold quality
bone marrow cell	CL:0002092	38.06	gold quality
duodenum	UBERON:0002114	37.43	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.78	gold quality
mucosa of transverse colon	UBERON:0004991	34.38	gold quality
bone marrow	UBERON:0002371	33.79	gold quality
monocyte	CL:0000576	33.71	gold quality
leukocyte	CL:0000738	33.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	32.09	gold quality
mucosa of stomach	UBERON:0001199	32.03	gold quality
liver	UBERON:0002107	31.73	gold quality
tonsil	UBERON:0002372	30.42	gold quality
prefrontal cortex	UBERON:0000451	30.13	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
corpus callosum	UBERON:0002336	29.80	gold quality
blood	UBERON:0000178	29.24	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	28.82	gold quality
right uterine tube	UBERON:0001302	28.78	gold quality
gall bladder	UBERON:0002110	28.33	gold quality
lymph node	UBERON:0000029	27.57	gold quality
placenta	UBERON:0001987	27.52	gold quality
endometrium	UBERON:0001295	27.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting ZC3H11C, 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-4481	100.00	66.42	1669
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zc3h11a	ENSDARG00000009754
mus_musculus	Zc3h11a	ENSMUSG00000102976
rattus_norvegicus		ENSRNOG00000066862
rattus_norvegicus		ENSRNOG00000075060
rattus_norvegicus		ENSRNOG00000085640

Paralogs (3): ZC3H11A (ENSG00000058673), C12orf50 (ENSG00000165805), ZC3H11B (ENSG00000215817)

Protein

Protein identifiers

Zinc finger CCCH domain-containing protein 11C — P0DQW0 (reviewed: P0DQW0)

All UniProt accessions (2): A0A8V8TLD8, P0DQW0

RefSeq proteins (1): NP_001258604* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR041686	Znf-CCCH_3	Domain

Pfam: PF15663

UniProt features (18 total): compositionally biased region 9, region of interest 6, zinc finger region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DQW0-F1	56.43	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): chr6q12, GOBP_NUCLEAR_TRANSPORT, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_NUCLEAR_EXPORT, GOBP_RNA_LOCALIZATION, GOMF_MRNA_BINDING, GOBP_RNA_EXPORT_FROM_NUCLEUS, GOBP_MRNA_EXPORT_FROM_NUCLEUS, GOBP_POLY_A_PLUS_MRNA_EXPORT_FROM_NUCLEUS, GOBP_INTRACELLULAR_TRANSPORT, GOBP_MRNA_TRANSPORT, GOBP_ESTABLISHMENT_OF_RNA_LOCALIZATION, MIR559, MIR4306, MIR4260

GO Biological Process (1): poly(A)+ mRNA export from nucleus (GO:0016973)

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mRNA export from nucleus	1
transition metal ion binding	1
cation binding	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTU1, A2AUY4, B7ZS37, D3Z8Y2, D4A4L4, D4A666, E1B7L7, O46385, O60293, O75152, O95425, P0DQW0, Q08AZ1, Q3KQW7, Q3U1C4, Q3UH68, Q3ZC82, Q4G0F8, Q4V9H5, Q5F3Z9, Q5NBX1, Q5REG6, Q5ZJJ1, Q5ZM88, Q61464, Q62394, Q68FE9, Q6NZF1, Q6PJT7, Q6ZQ03, Q6ZU65, Q76L83, Q7TMD5, Q8BHZ4, Q8BJ05, Q8BLG0, Q8BZ32, Q8C9B9, Q8CCJ9, Q8K298

Diamond homologs: A0A1B0GTU1, O75152, P0DQW0, Q32KY7, Q4R731, Q5REG6, Q5ZJJ1, Q6AYU0, Q6NZF1, Q8NA57, Q6K977

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
536	NM_001142800.1(EYS):c.1767-24596_2023+238135del	Pathogenic

SpliceAI

46 predictions. Top by Δscore:

Variant	Effect	Δscore
6:65306283:A:C	acceptor_gain	0.7100
6:65301731:T:TA	donor_gain	0.6500
6:65303124:AGTC:A	acceptor_gain	0.5000
6:65303062:AC:A	donor_gain	0.4300
6:65303063:CC:C	donor_gain	0.4300
6:65303065:C:T	donor_gain	0.3900
6:65303125:GTC:G	acceptor_gain	0.3900
6:65303060:C:T	donor_gain	0.3800
6:65304581:G:C	donor_gain	0.3800
6:65303064:CC:C	donor_gain	0.3500
6:65303206:T:C	donor_gain	0.3500
6:65306347:C:A	acceptor_gain	0.3300
6:65303122:GCAGT:G	acceptor_gain	0.3200
6:65303123:CAGTC:C	acceptor_gain	0.3200
6:65303130:T:A	acceptor_gain	0.3200
6:65303150:T:A	acceptor_gain	0.3200
6:65304066:A:C	acceptor_gain	0.3100
6:65303257:C:G	acceptor_gain	0.3000
6:65303291:T:A	acceptor_gain	0.3000
6:65306271:CT:C	acceptor_gain	0.3000
6:65306272:TT:T	acceptor_gain	0.3000
6:65306346:AC:A	acceptor_gain	0.3000
6:65303256:CCCT:C	acceptor_gain	0.2900
6:65306546:T:G	acceptor_gain	0.2900
6:65303126:T:A	acceptor_gain	0.2800
6:65306545:T:TG	acceptor_gain	0.2800
6:65303288:ATGT:A	acceptor_gain	0.2700
6:65304254:TGAC:T	donor_gain	0.2700
6:65306272:T:C	acceptor_gain	0.2700
6:65301783:C:CA	donor_gain	0.2600

AlphaMissense

5239 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000052502 (6:65301081 G>A,C), RS1001821607 (6:65301577 G>A), RS1003713184 (6:65305349 C>T), RS1003785081 (6:65305870 G>GA), RS1005568712 (6:65305956 G>A), RS1006319948 (6:65302720 T>A), RS1007275910 (6:65304523 C>A,T), RS1007348341 (6:65306571 T>A,G), RS1008158688 (6:65303561 C>G), RS1009807110 (6:65304835 G>A), RS1010142602 (6:65301288 G>A), RS1010713458 (6:65307048 C>T), RS1014359128 (6:65300476 T>A,G), RS1014571682 (6:65302907 C>G,T), RS1015072244 (6:65301701 A>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:602772

GenCC curated gene-disease

Mondo (1): retinitis pigmentosa 25 (MONDO:0011272)

Orphanet (1): Retinitis pigmentosa (Orphanet:791)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566425	Retinitis Pigmentosa 25 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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