ZC3H11D

Summary

ZC3H11D (zinc finger CCCH-type containing 11D, HGNC:26665) is a protein-coding gene on chromosome 12q21.32, encoding Uncharacterized protein C12orf50 (Q8NA57).

Predicted to be involved in poly(A)+ mRNA export from nucleus.

Source: NCBI Gene 160419 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_152589

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26665
Approved symbol	ZC3H11D
Name	zinc finger CCCH-type containing 11D
Location	12q21.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35821
Ensembl gene	ENSG00000165805
Ensembl biotype	protein_coding
Entrez	160419

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000298699, ENST00000546547, ENST00000550553, ENST00000551163, ENST00000551944

RefSeq mRNA: 2 — MANE Select: NM_152589 NM_001363616, NM_152589

CCDS: CCDS86321, CCDS9031

Canonical transcript exons

ENST00000298699 — 13 exons

Exon	Start	End
ENSE00001096752	87987850	87987966
ENSE00001096758	87985850	87986053
ENSE00001096764	87983103	87983195
ENSE00001235924	88029340	88029401
ENSE00001235939	87980035	87980356
ENSE00003478194	88026951	88027070
ENSE00003571157	88026488	88026608
ENSE00003604318	87994633	87994743
ENSE00003605554	87996569	87996646
ENSE00003656984	87989264	87989371
ENSE00003661999	87996374	87996487
ENSE00003674832	87986312	87986416
ENSE00003783995	87998035	87998190

Expression profiles

Bgee: expression breadth ubiquitous, 114 present calls, max score 96.69.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0696 / max 58.6410, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132399	0.0387	3
132398	0.0309	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.69	gold quality
left testis	UBERON:0004533	92.80	gold quality
right testis	UBERON:0004534	92.52	gold quality
testis	UBERON:0000473	89.76	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.26	gold quality
adult organism	UBERON:0007023	73.84	gold quality
pancreatic ductal cell	CL:0002079	62.44	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	58.83	silver quality
stromal cell of endometrium	CL:0002255	58.63	gold quality
tibialis anterior	UBERON:0001385	56.17	silver quality
sural nerve	UBERON:0015488	55.29	gold quality
epithelial cell of pancreas	CL:0000083	54.95	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
cortical plate	UBERON:0005343	51.65	gold quality
myocardium	UBERON:0002349	50.25	gold quality
ganglionic eminence	UBERON:0004023	49.95	silver quality
ileal mucosa	UBERON:0000331	48.22	silver quality
ventricular zone	UBERON:0003053	48.21	gold quality
deltoid	UBERON:0001476	48.18	gold quality
colonic epithelium	UBERON:0000397	48.00	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.64	gold quality
right coronary artery	UBERON:0001625	46.41	gold quality
mucosa of stomach	UBERON:0001199	46.20	gold quality
cauda epididymis	UBERON:0004360	46.15	gold quality
cerebellar cortex	UBERON:0002129	45.86	silver quality
cerebellar hemisphere	UBERON:0002245	45.80	silver quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.69
E-MTAB-6678	no	546.06
E-MTAB-8911	no	277.81
E-CURD-89	no	41.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting ZC3H11D, 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-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6758-3P	99.57	67.55	1078
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-508-3P	98.66	69.62	887
HSA-MIR-5094	98.63	67.11	1062
HSA-MIR-1245B-3P	98.01	68.91	1387

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zc3h11a	ENSDARG00000009754
mus_musculus	1700017N19Rik	ENSMUSG00000056912
rattus_norvegicus	C7h12orf50	ENSRNOG00000051928

Paralogs (3): ZC3H11A (ENSG00000058673), ZC3H11C (ENSG00000214558), ZC3H11B (ENSG00000215817)

Protein

Protein identifiers

Uncharacterized protein C12orf50 — Q8NA57 (reviewed: Q8NA57)

All UniProt accessions (3): Q8NA57, F8VSD7, F8VXH4

RefSeq proteins (2): NP_001350545, NP_689802* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040943	DUF5571	Family
IPR041686	Znf-CCCH_3	Domain

Pfam: PF15663, PF17732

UniProt features (8 total): region of interest 3, compositionally biased region 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NA57-F1	53.35	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, FREAC2_01, TGACCTY_ERR1_Q2, FOXO4_01, FOXO1_01, GOBP_NUCLEAR_TRANSPORT, chr12q21, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, HNF1_C, IK2_01, HAND1E47_01, GOBP_NUCLEAR_EXPORT, GATA4_Q3, IK3_01, FREAC7_01

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

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mRNA export from nucleus	1
binding	1

Protein interactions and networks

STRING

558 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZC3H11D	RLIG1	Q8N999	605
ZC3H11D	CXorf65	A6NEN9	518
ZC3H11D	CCDC187	A0A096LP49	507
ZC3H11D	TMCO2	Q7Z6W1	507
ZC3H11D	C20orf173	Q96LM9	507
ZC3H11D	FAM209A	Q5JX71	505
ZC3H11D	CCDC54	Q8NEL0	480
ZC3H11D	CIMIP4	O43247	479
ZC3H11D	SPATA31G1	Q5VYM1	449
ZC3H11D	C22orf23	Q9BZE7	447
ZC3H11D	FAM81B	Q96LP2	443
ZC3H11D	GARIN1B	Q96KD3	418
ZC3H11D	SHCBP1L	Q9BZQ2	418
ZC3H11D	CABS1	Q96KC9	417
ZC3H11D	CFAP206	Q8IYR0	416

IntAct

10 interactions, top by confidence:

A	B	Type	Score
GOLGA2	C12orf50	psi-mi:“MI:0915”(physical association)	0.780
C12orf50	GAPDHS	psi-mi:“MI:0915”(physical association)	0.590
C12orf50	GOLGA2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): C12orf50 (Two-hybrid), GAPDHS (Affinity Capture-MS), GOLGA2 (Two-hybrid), GAPDHS (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q2UEI8, A0JNH9, A2BIL8, A8PUI7, B1H1S4, B2GUZ2, E7FAP1, E9Q309, F1R983, O60284, P49452, P51960, P86345, Q0P5H2, Q3T0A6, Q3T8J9, Q4KLP8, Q4QY64, Q4R731, Q535K8, Q563C3, Q58EL7, Q5FBB7, Q5QJE6, Q5VT06, Q5XG21, Q65Z40, Q6KAQ7, Q6NWJ0, Q6P0N0, Q6P6I6, Q76FK4, Q7YQM1, Q7YQM2, Q80WQ8, Q8C263, Q8C551, Q8IYH5, Q8NA57, Q8R2M2

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1370 predictions. Top by Δscore:

Variant	Effect	Δscore
12:87986051:CTG:C	acceptor_gain	1.0000
12:87986054:C:CC	acceptor_gain	1.0000
12:87986306:CCTTA:C	donor_loss	1.0000
12:87986307:CTTA:C	donor_loss	1.0000
12:87986308:TTACC:T	donor_loss	1.0000
12:87986309:TACCT:T	donor_loss	1.0000
12:87986310:A:C	donor_loss	1.0000
12:87986311:C:G	donor_loss	1.0000
12:87986311:CCT:C	donor_gain	1.0000
12:87986311:CCTCT:C	donor_gain	1.0000
12:87986412:ATTCA:A	acceptor_gain	1.0000
12:87986413:TTCA:T	acceptor_gain	1.0000
12:87986415:CA:C	acceptor_gain	1.0000
12:87986415:CAC:C	acceptor_loss	1.0000
12:87986415:CACT:C	acceptor_gain	1.0000
12:87986416:ACT:A	acceptor_loss	1.0000
12:87986417:C:CC	acceptor_gain	1.0000
12:87986418:T:C	acceptor_gain	1.0000
12:87986418:T:TC	acceptor_gain	1.0000
12:87987848:A:AC	donor_gain	1.0000
12:87987849:C:CC	donor_gain	1.0000
12:87994628:CTCA:C	donor_loss	1.0000
12:87994629:TCACC:T	donor_loss	1.0000
12:87994630:CACCT:C	donor_loss	1.0000
12:87994631:A:AC	donor_gain	1.0000
12:87994631:ACCT:A	donor_gain	1.0000
12:87994631:ACCTC:A	donor_gain	1.0000
12:87994632:C:CC	donor_gain	1.0000
12:87994632:C:CT	donor_loss	1.0000
12:87994632:CCT:C	donor_gain	1.0000

AlphaMissense

2749 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:88026540:A:C	F27L	0.998
12:88026540:A:T	F27L	0.998
12:88026542:A:G	F27L	0.998
12:88026548:A:G	C25R	0.998
12:88026582:C:A	W13C	0.998
12:88026582:C:G	W13C	0.998
12:88026590:A:G	C11R	0.998
12:88026523:C:G	R33P	0.997
12:88026546:A:C	C25W	0.997
12:88026547:C:T	C25Y	0.997
12:88026563:A:G	C20R	0.997
12:88026584:A:G	W13R	0.997
12:88026584:A:T	W13R	0.997
12:88026588:G:C	C11W	0.997
12:88026534:G:C	H29Q	0.996
12:88026534:G:T	H29Q	0.996
12:88026536:G:C	H29D	0.996
12:88026589:C:T	C11Y	0.996
12:88026547:C:G	C25S	0.995
12:88026548:A:T	C25S	0.995
12:88026562:C:G	C20S	0.995
12:88026563:A:T	C20S	0.995
12:88026589:C:G	C11S	0.995
12:88026590:A:T	C11S	0.995
12:88026502:A:G	L40S	0.994
12:88026547:C:A	C25F	0.994
12:88026504:A:C	F39L	0.993
12:88026504:A:T	F39L	0.993
12:88026506:A:G	F39L	0.993
12:88026561:A:C	C20W	0.993

dbSNP variants (sampled 300 via entrez): RS1000024193 (12:88009479 T>A), RS1000058034 (12:87991788 G>A), RS1000077536 (12:88011370 T>C), RS1000096815 (12:88028342 T>A,C), RS1000256812 (12:87991458 G>A), RS1000355334 (12:88004764 A>G), RS1000387745 (12:88004945 C>A,T), RS1000433427 (12:88017235 T>A), RS1000489192 (12:87984947 C>T), RS1000525618 (12:88017019 A>G), RS1000561378 (12:88010454 T>A), RS1000641215 (12:87998214 A>G), RS1000660321 (12:87980025 T>A), RS1000750926 (12:88016855 G>A), RS1000787206 (12:87999754 T>C)

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
GCST002595_19	Clozapine-induced agranulocytosis	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
abrine	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	affects cotreatment, decreases expression	1
Cadmium	decreases reaction, increases abundance, increases palmitoylation	1
Lipopolysaccharides	increases expression, affects response to substance, affects cotreatment	1
Plant Extracts	affects cotreatment, decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases reaction, increases abundance, increases palmitoylation	1

Clinical trials (associated diseases)

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