ZC3H11B

Summary

ZC3H11B (zinc finger CCCH-type containing 11B, HGNC:25659) is a protein-coding gene on chromosome 1q41, encoding Zinc finger CCCH domain-containing protein 11B (A0A1B0GTU1). May play a role in mRNA transport.

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

Source: NCBI Gene 643136 — RefSeq curated summary.

At a glance

• GWAS associations: 49
• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001355457

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25659
Approved symbol	ZC3H11B
Name	zinc finger CCCH-type containing 11B
Location	1q41
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000215817
Ensembl biotype	protein_coding
Entrez	643136

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000651890

RefSeq mRNA: 1 — MANE Select: NM_001355457 NM_001355457

CCDS: CCDS86051

Canonical transcript exons

ENST00000651890 — 2 exons

Exon	Start	End
ENSE00003844378	219608012	219612563
ENSE00003847018	219612931	219613105

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 77.40.

Top tissues by expression

130 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	77.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.32	gold quality
testis	UBERON:0000473	70.62	gold quality
right testis	UBERON:0004534	70.60	gold quality
left testis	UBERON:0004533	70.25	gold quality
ventricular zone	UBERON:0003053	61.03	gold quality
ganglionic eminence	UBERON:0004023	60.11	gold quality
hindlimb stylopod muscle	UBERON:0004252	58.43	gold quality
stromal cell of endometrium	CL:0002255	58.04	gold quality
cortical plate	UBERON:0005343	55.86	gold quality
heart left ventricle	UBERON:0002084	53.78	gold quality
gastrocnemius	UBERON:0001388	53.03	gold quality
muscle of leg	UBERON:0001383	52.98	gold quality
lower esophagus mucosa	UBERON:0035834	52.87	gold quality
right lobe of liver	UBERON:0001114	52.19	silver quality
lymph node	UBERON:0000029	50.73	silver quality
granulocyte	CL:0000094	50.55	silver quality
primary visual cortex	UBERON:0002436	50.28	gold quality
leukocyte	CL:0000738	50.11	silver quality
mucosa of transverse colon	UBERON:0004991	49.68	gold quality
vermiform appendix	UBERON:0001154	49.66	gold quality
heart	UBERON:0000948	49.47	gold quality
islet of Langerhans	UBERON:0000006	49.35	gold quality
monocyte	CL:0000576	49.32	silver quality
blood	UBERON:0000178	49.02	gold quality
right coronary artery	UBERON:0001625	48.97	gold quality
left adrenal gland cortex	UBERON:0035825	48.97	gold quality
left adrenal gland	UBERON:0001234	48.96	gold quality
duodenum	UBERON:0002114	48.89	gold quality
skeletal muscle tissue	UBERON:0001134	48.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.17

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Genetic variants in ZC3H11B, RSPO1, and GJD2 are associated with susceptibility to the development of high myopia in a Han Chinese population. (PMID:26485405)
• Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities. (PMID:31300455)

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), ZC3H11C (ENSG00000214558)

Protein

Protein identifiers

Zinc finger CCCH domain-containing protein 11B — A0A1B0GTU1 (reviewed: A0A1B0GTU1)

All UniProt accessions (1): A0A1B0GTU1

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in mRNA transport.

RefSeq proteins (1): NP_001342386* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR041686	Znf-CCCH_3	Domain

Pfam: PF15663

UniProt features (19 total): compositionally biased region 9, region of interest 6, zinc finger region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTU1-F1	56.23	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): 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, LAMB3_TARGET_GENES, THAKAR_PBMC_INACTIVATED_INFLUENZA_AGE_21_30YO_RESPONDERS_28DY_UP, GOBP_NITROGEN_COMPOUND_TRANSPORT, GOBP_ESTABLISHMENT_OF_LOCALIZATION_IN_CELL

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

346 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZC3H11B	CMSS1	Q9BQ75	734
ZC3H11B	GJD2	Q9UKL4	623
ZC3H11B	SNTB1	Q13884	574
ZC3H11B	ALPG	P10696	571
ZC3H11B	LAMA2	P24043	507
ZC3H11B	ZNRF3	Q9ULT6	507
ZC3H11B	PRSS56	P0CW18	479
ZC3H11B	ZNF644	Q9H582	447
ZC3H11B	KCNQ5	Q9NR82	419
ZC3H11B	RSPO1	Q2MKA7	418
ZC3H11B	ZNF345	Q14585	400
ZC3H11B	MPP4	Q96JB8	398
ZC3H11B	LYPLAL1	Q5VWZ2	390
ZC3H11B	CD55	P08174	356
ZC3H11B	EDF1	O60869	353
ZC3H11B	NFAT5	O94916	353

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

5242 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:219611817:G:C	F82L	0.993
1:219611817:G:T	F82L	0.993
1:219611819:A:G	F82L	0.993
1:219611999:A:G	C22R	0.992
1:219611991:G:C	F24L	0.991
1:219611991:G:T	F24L	0.991
1:219611993:A:G	F24L	0.991
1:219612015:A:C	C16W	0.990
1:219612017:A:G	C16R	0.990
1:219612016:C:G	C16S	0.989
1:219612017:A:T	C16S	0.989
1:219612033:A:C	F10L	0.988
1:219612033:A:T	F10L	0.988
1:219612035:A:G	F10L	0.988
1:219611997:G:C	C22W	0.987
1:219612016:C:T	C16Y	0.987
1:219612041:A:G	C8R	0.987
1:219611998:C:G	C22S	0.985
1:219611998:C:T	C22Y	0.985
1:219611999:A:T	C22S	0.985
1:219612039:G:C	C8W	0.985
1:219611907:A:C	F52L	0.983
1:219611907:A:T	F52L	0.983
1:219611909:A:G	F52L	0.983
1:219611954:A:G	C37R	0.983
1:219612040:C:G	C8S	0.983
1:219612041:A:T	C8S	0.983
1:219611866:C:G	C66S	0.982
1:219611867:A:G	C66R	0.982
1:219611867:A:T	C66S	0.982

dbSNP variants (sampled 300 via entrez): RS1000159774 (1:219613885 A>G), RS1000720775 (1:219614151 A>T), RS1000722462 (1:219607788 T>G), RS1000947571 (1:219612123 A>G), RS1001433347 (1:219613279 AG>A), RS1002410115 (1:219611585 C>A,T), RS1002439558 (1:219611212 A>C), RS1003395417 (1:219608901 A>C,G), RS1003427841 (1:219608484 T>A,G), RS1004380561 (1:219610517 A>G), RS1004688719 (1:219614476 C>T), RS1004982748 (1:219608037 A>T), RS1005086529 (1:219607556 C>A), RS1005751059 (1:219614763 A>G,T), RS1005787029 (1:219614500 T>A)

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

49 associations (top):

Study	Trait	p-value
GCST001561_4	Myopia (pathological)	3.000000e-10
GCST002063_9	Sexual dimorphism in anthropometric traits	7.000000e-16
GCST002115_5	Axial length	1.000000e-11
GCST004067_176	Hip circumference adjusted for BMI	3.000000e-08
GCST004067_192	Hip circumference adjusted for BMI	4.000000e-35
GCST004067_79	Hip circumference adjusted for BMI	1.000000e-35
GCST005414_19	Type 2 diabetes	3.000000e-08
GCST007157_5	Corneal astigmatism	4.000000e-10
GCST007159_19	Corneal astigmatism	5.000000e-14
GCST007160_1	Refractive astigmatism	2.000000e-07
GCST009764_14	Body mass index	4.000000e-08
GCST010994_3	High myopia	2.000000e-11
GCST012226_421	Waist circumference adjusted for body mass index	9.000000e-11
GCST012226_422	Waist circumference adjusted for body mass index	4.000000e-10
GCST012227_1213	Hip circumference adjusted for BMI	9.000000e-23
GCST012227_1214	Hip circumference adjusted for BMI	1.000000e-16
GCST012227_1215	Hip circumference adjusted for BMI	1.000000e-11
GCST012227_1218	Hip circumference adjusted for BMI	5.000000e-14
GCST012227_1219	Hip circumference adjusted for BMI	1.000000e-11
GCST012229_20	Hip index	2.000000e-11
GCST012229_30	Hip index	2.000000e-13
GCST012231_161	A body shape index	2.000000e-08
GCST90020024_641	A body shape index	4.000000e-16
GCST90020024_646	A body shape index	2.000000e-09
GCST90020025_1279	Waist-to-hip ratio adjusted for BMI	2.000000e-12
GCST90020025_1281	Waist-to-hip ratio adjusted for BMI	2.000000e-08
GCST90020025_1282	Waist-to-hip ratio adjusted for BMI	2.000000e-30
GCST90020025_1283	Waist-to-hip ratio adjusted for BMI	3.000000e-38
GCST90020025_1321	Waist-to-hip ratio adjusted for BMI	2.000000e-37
GCST90020026_692	Hip index	3.000000e-26

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004207	pathological myopia
EFO:0004343	waist-hip ratio
EFO:0005951	sexual dimorphism
EFO:0005318	axial length measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:1002040	Corneal astigmatism
EFO:0004340	body mass index
EFO:0007789	BMI-adjusted waist circumference
EFO:0007788	BMI-adjusted waist-hip ratio

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
methylparaben	increases expression	1
sodium arsenite	increases expression	1
Doxorubicin	decreases expression	1

Clinical trials (associated diseases)

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