ZC3H7B

gene
On this page

Also known as RoXaNFLJ13787DKFZp434K0920KIAA1031

Summary

ZC3H7B (zinc finger CCCH-type containing 7B, HGNC:30869) is a protein-coding gene on chromosome 22q13.2, encoding Zinc finger CCCH domain-containing protein 7B (Q9UGR2). May be a specific regulator of miRNA biogenesis.

This gene encodes a protein that contains a tetratricopeptide repeat domain. The encoded protein also interacts with the rotavirus non-structural protein NSP3.

Source: NCBI Gene 23264 — RefSeq curated summary.

At a glance

  • GWAS associations: 22
  • Clinical variants (ClinVar): 143 total
  • MANE Select transcript: NM_017590

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30869
Approved symbolZC3H7B
Namezinc finger CCCH-type containing 7B
Location22q13.2
Locus typegene with protein product
StatusApproved
AliasesRoXaN, FLJ13787, DKFZp434K0920, KIAA1031
Ensembl geneENSG00000100403
Ensembl biotypeprotein_coding
OMIM618206
Entrez23264

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 retained_intron

ENST00000352645, ENST00000486331, ENST00000897616, ENST00000897617, ENST00000897618, ENST00000897619, ENST00000897620, ENST00000926343

RefSeq mRNA: 1 — MANE Select: NM_017590 NM_017590

CCDS: CCDS14013

Canonical transcript exons

ENST00000352645 — 23 exons

ExonStartEnd
ENSE000006556484133900141339191
ENSE000006556564133981641340137
ENSE000006556664134108841341146
ENSE000006556754134252941342628
ENSE000006556834134341541343576
ENSE000006556854134600341346208
ENSE000006556904134806741348167
ENSE000006556974134912041349301
ENSE000006557174135546941355602
ENSE000006557234135575741355862
ENSE000006557264135595441356062
ENSE000006557284135634341356476
ENSE000006557314135664541356808
ENSE000009112934133217141332227
ENSE000012430744135156141351646
ENSE000013073634130152541301772
ENSE000013092764135717741360147
ENSE000013820584133831341338355
ENSE000034785214132720641327364
ENSE000035343854132556441325597
ENSE000035463364133002341330103
ENSE000035510944132572141325918
ENSE000036289794132065541320713

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 99.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 65.6698 / max 614.6223, expressed in 1821 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
19246062.06001821
1924592.47901224
1924580.5883326
1924650.3302146
1924610.212478

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011599.32gold quality
buccal mucosa cellCL:000233699.22gold quality
nippleUBERON:000203098.99gold quality
renal medullaUBERON:000036298.95gold quality
cardia of stomachUBERON:000116298.95gold quality
pylorusUBERON:000116698.75gold quality
superior surface of tongueUBERON:000737198.60gold quality
ventral tegmental areaUBERON:000269198.51gold quality
spermCL:000001998.42gold quality
trigeminal ganglionUBERON:000167598.41gold quality
dorsal root ganglionUBERON:000004498.13gold quality
superior vestibular nucleusUBERON:000722798.07gold quality
pericardiumUBERON:000240798.06gold quality
saphenous veinUBERON:000731898.06gold quality
periodontal ligamentUBERON:000826698.01gold quality
male germ cellCL:000001597.99gold quality
inferior vagus X ganglionUBERON:000536397.94gold quality
pharyngeal mucosaUBERON:000035597.89gold quality
visceral pleuraUBERON:000240197.58gold quality
cervix squamous epitheliumUBERON:000692297.52gold quality
tracheaUBERON:000312697.42gold quality
vena cavaUBERON:000408797.28gold quality
subthalamic nucleusUBERON:000190697.25gold quality
penisUBERON:000098997.23gold quality
body of tongueUBERON:001187697.14gold quality
mucosa of paranasal sinusUBERON:000503097.05gold quality
urethraUBERON:000005797.03gold quality
blood vessel layerUBERON:000479797.03gold quality
ponsUBERON:000098897.01gold quality
tendon of biceps brachiiUBERON:000818896.76gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no4.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

175 targeting ZC3H7B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-8485100.0077.574731
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-656-3P100.0072.152788
HSA-MIR-1212199.9966.64255
HSA-MIR-520G-5P99.9966.76658
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-9-3P99.9670.882068
HSA-MIR-365899.9673.874379
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-426799.9666.532368
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-185-3P99.9567.011743
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-61399.9171.501710
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-627-3P99.9071.423316
HSA-MIR-17-5P99.8973.832665
HSA-MIR-153-5P99.8973.866317
HSA-MIR-106B-5P99.8874.722795

Literature-anchored findings (GeneRIF, showing 6)

  • RoXaN is capable of interacting with NSP3 and eIF4G I in vivo and during rotavirus infection. Domains of interaction were mapped. (PMID:15047801)
  • nuclear localization of PABP-C1 not only is dependent on the capacity of rotavirus NSP3 to interact with eIF4G but also requires the interaction of NSP3 with a specific region in RoXaN (PMID:18799579)
  • Reverse transciptase-PCR with the ZC3H7B forward and BCOR reverse primer combinations confirmed the presence of a ZC3H7-BCOR chimeric transcript in both ESS carrying a der(22)t(X;22) but not in a control ESS with t(1;6) and the MEAF6-PHF1 fusion. (PMID:23580382)
  • ZC3H7B-BCOR and MEAF6-PHF1 fusions occurred predominantly in S100 protein-negative and malignant ossifying fibromyxoid tumors. (PMID:24285434)
  • The present study further expands the genetic spectrum of small blue round cell tumors, with 2 novel fusions, BCOR-MAML3 and ZC3H7B-BCOR, identified (PMID:26752546)
  • we find that ESS with ZC3H7B-BCOR fusion constitutes a novel type of high-grade endometrial stromal sarcoma and shares significant morphologic overlap with myxoid leiomyosarcoma. (PMID:27631520)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriozc3h7bbENSDARG00000055930
danio_reriozc3h7baENSDARG00000098540
mus_musculusZc3h7bENSMUSG00000022390
rattus_norvegicusZc3h7bENSRNOG00000055925

Paralogs (1): ZC3H7A (ENSG00000122299)

Protein

Protein identifiers

Zinc finger CCCH domain-containing protein 7BQ9UGR2 (reviewed: Q9UGR2)

Alternative names: Rotavirus ‘X’-associated non-structural protein

All UniProt accessions (1): Q9UGR2

UniProt curated annotations — full annotation on UniProt →

Function. May be a specific regulator of miRNA biogenesis. Binds to microRNAs MIR7-1, MIR16-2 and MIR29A hairpins recognizing the ‘ATA(A/T)’ motif in the apical loop.

Subunit / interactions. (Microbial infection) Interacts (via LD motif) with rotavirus A NSP3 (via the coiled-coil region).

Subcellular location. Nucleus.

RefSeq proteins (1): NP_060060* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000571Znf_CCCHDomain
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR019734TPR_rptRepeat
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR036855Znf_CCCH_sfHomologous_superfamily
IPR039691ZC3H7A/BFamily

Pfam: PF00642, PF13181

UniProt features (26 total): sequence conflict 9, zinc finger region 5, repeat 3, modified residue 3, mutagenesis site 2, chain 1, short sequence motif 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UGR2-F170.240.25

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 217, 364, 367

Mutagenesis-validated functional residues (2):

PositionPhenotype
241–243almost no effect on nsp3 binding.
252–254complete loss of nsp3 binding.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 104 (showing top): TAATAAT_MIR126, TATTATA_MIR374, CACCAGC_MIR138, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, CAGCAGG_MIR370, BLALOCK_ALZHEIMERS_DISEASE_UP, TCCCCAC_MIR491, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GAL_LEUKEMIC_STEM_CELL_UP, chr22q13, CAGCTTT_MIR320, GOMF_MIRNA_BINDING, LIU_COMMON_CANCER_GENES, CACTGCC_MIR34A_MIR34C_MIR449, LEE_DIFFERENTIATING_T_LYMPHOCYTE

GO Biological Process (2): post-transcriptional regulation of gene expression (GO:0010608), miRNA processing (GO:0035196)

GO Molecular Function (5): RNA binding (GO:0003723), zinc ion binding (GO:0008270), miRNA binding (GO:0035198), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of gene expression1
regulatory ncRNA processing1
nucleic acid binding1
transition metal ion binding1
regulatory RNA binding1
binding1
cation binding1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1941 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZC3H7BSH2D3CQ8N5H7825
ZC3H7BCCNB3Q8WWL7726
ZC3H7BNUTM2AQ8IVF1682
ZC3H7BMEAF6Q9HAF1668
ZC3H7BYWHAEP29360630
ZC3H7BPHF1O43189628
ZC3H7BJAZF1Q86VZ6623
ZC3H7BEZHIPQ86X51611
ZC3H7BNUTM2BA6NNL0603
ZC3H7BPCGF1Q9BSM1593
ZC3H7BMAML3Q96JK9588
ZC3H7BMBTD1Q05BQ5575
ZC3H7BNUTM2GQ5VZR2531
ZC3H7BBCORL1Q5H9F3478
ZC3H7BDUX4L2P0CJ85477

IntAct

35 interactions, top by confidence:

ABTypeScore
ZC3H7Bpsi-mi:“MI:0915”(physical association)0.580
ZC3H7Bpsi-mi:“MI:0915”(physical association)0.580
ZC3H7BEIF4G1psi-mi:“MI:0915”(physical association)0.570
NNOP56psi-mi:“MI:0914”(association)0.530
NRBM47psi-mi:“MI:0914”(association)0.530
RPS3ZNF316psi-mi:“MI:0914”(association)0.530
EIF4G1psi-mi:“MI:0915”(physical association)0.480
EIF4G1psi-mi:“MI:0914”(association)0.480
ZC3H7BZNF638psi-mi:“MI:0915”(physical association)0.400
ZC3H7BDDX21psi-mi:“MI:0915”(physical association)0.400
HSP90AB1ZC3H7Bpsi-mi:“MI:0915”(physical association)0.400
ZC3H7BMLF1psi-mi:“MI:0915”(physical association)0.400
ZC3H7BAARSD1psi-mi:“MI:0915”(physical association)0.400
JUNTPM3psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
NIGF2BP3psi-mi:“MI:0914”(association)0.350
NRBM47psi-mi:“MI:0914”(association)0.350
MYCpsi-mi:“MI:0914”(association)0.350
HNRNPCL2SMCHD1psi-mi:“MI:0914”(association)0.350
EEF1AKMT3SMCHD1psi-mi:“MI:0914”(association)0.350

BioGRID (73): ZC3H7B (Affinity Capture-RNA), ZC3H7B (Affinity Capture-RNA), ZC3H7B (Affinity Capture-RNA), ZC3H7B (Affinity Capture-MS), ZC3H7B (Affinity Capture-RNA), ZC3H7B (Proximity Label-MS), ZC3H7B (Affinity Capture-MS), ZC3H7B (Affinity Capture-MS), ZC3H7B (Affinity Capture-MS), ZC3H7B (Protein-RNA), ZC3H7B (Protein-RNA), ZC3H7B (Protein-RNA), ZC3H7B (Protein-RNA), ZC3H7B (Proximity Label-MS), ZC3H7B (Proximity Label-MS)

ESM2 similar proteins: A0A0G2JV04, B0V207, D3Z8X7, D3ZFJ3, D3ZND0, F1LM81, G9CGD6, O00499, O08539, O08839, O12940, O60308, O60784, O75674, O88746, P42567, P55194, Q05DH4, Q0GNC1, Q0IHV1, Q27J81, Q3B7M3, Q3UN70, Q4KLN4, Q505K2, Q5FVK6, Q5T0F9, Q5U3K5, Q66HA5, Q68EF0, Q6P1N0, Q6P5E6, Q6P9Q4, Q6P9Q6, Q80V31, Q80V94, Q8BMI3, Q8BRN9, Q8K1A6, Q8R0H9

Diamond homologs: A4K2V0, A6HD62, D7REX8, F4IRM4, F4JTI1, F4K487, O13754, O14217, O35814, O48802, O54981, O94826, P23231, P31948, P33313, P38825, P53041, P53042, Q07617, Q28IV3, Q2U919, Q32PZ3, Q38931, Q3KRD5, Q3ZBR5, Q3ZBZ8, Q43207, Q496Y0, Q4R8N7, Q54DA8, Q54IP0, Q5RAP0, Q5U2X2, Q5VJS5, Q5ZHY5, Q60676, Q60864, Q68F64, Q68FQ7, Q6DGE9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance119
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3793 predictions. Top by Δscore:

VariantEffectΔscore
22:41301641:G:GTdonor_gain1.0000
22:41320653:A:AGacceptor_gain1.0000
22:41320654:G:GGacceptor_gain1.0000
22:41320654:GA:Gacceptor_gain1.0000
22:41320714:G:GGdonor_gain1.0000
22:41325597:GG:Gdonor_loss1.0000
22:41325598:GT:Gdonor_loss1.0000
22:41325599:T:Gdonor_loss1.0000
22:41325916:ATGG:Adonor_loss1.0000
22:41325917:TGGT:Tdonor_loss1.0000
22:41325919:G:GGdonor_gain1.0000
22:41325919:GTGA:Gdonor_loss1.0000
22:41325920:T:Gdonor_loss1.0000
22:41327200:T:TAacceptor_gain1.0000
22:41327201:G:Aacceptor_gain1.0000
22:41327201:GGCA:Gacceptor_loss1.0000
22:41327202:GCA:Gacceptor_loss1.0000
22:41327203:CA:Cacceptor_loss1.0000
22:41327204:A:AGacceptor_gain1.0000
22:41327204:AG:Aacceptor_gain1.0000
22:41327204:AGG:Aacceptor_gain1.0000
22:41327204:AGGGC:Aacceptor_loss1.0000
22:41327205:G:GAacceptor_gain1.0000
22:41327205:GG:Gacceptor_gain1.0000
22:41327205:GGG:Gacceptor_gain1.0000
22:41327205:GGGC:Gacceptor_gain1.0000
22:41327205:GGGCC:Gacceptor_gain1.0000
22:41327320:G:GTdonor_gain1.0000
22:41327361:CCAC:Cdonor_gain1.0000
22:41327362:CAC:Cdonor_gain1.0000

AlphaMissense

6455 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:41325737:T:CL35P1.000
22:41325749:T:CL39P1.000
22:41325760:G:CG43R1.000
22:41342593:T:CF421S1.000
22:41342604:T:CC425R1.000
22:41342605:G:AC425Y1.000
22:41342605:G:TC425F1.000
22:41342606:C:GC425W1.000
22:41342613:T:AC428S1.000
22:41342613:T:CC428R1.000
22:41342614:G:AC428Y1.000
22:41342614:G:CC428S1.000
22:41342615:C:GC428W1.000
22:41343462:T:AC449S1.000
22:41343462:T:CC449R1.000
22:41343463:G:CC449S1.000
22:41343464:C:GC449W1.000
22:41343513:T:AW466R1.000
22:41343513:T:CW466R1.000
22:41343525:C:GR470G1.000
22:41343549:T:CF478L1.000
22:41343550:T:CF478S1.000
22:41343550:T:GF478C1.000
22:41343551:C:AF478L1.000
22:41343551:C:GF478L1.000
22:41343556:G:AG480D1.000
22:41343561:T:GY482D1.000
22:41343570:T:AC485S1.000
22:41343570:T:CC485R1.000
22:41343570:T:GC485G1.000

dbSNP variants (sampled 300 via entrez): RS1000010921 (22:41357628 G>A,C), RS1000023413 (22:41349876 A>G), RS1000043465 (22:41357922 C>A,G), RS1000076835 (22:41351730 A>T), RS1000097745 (22:41327341 C>T), RS1000152653 (22:41312442 A>C,G), RS1000154049 (22:41325175 G>A,C), RS1000277535 (22:41331967 G>A), RS1000295923 (22:41344092 C>T), RS1000401912 (22:41330187 G>A,T), RS1000449778 (22:41318104 C>T), RS1000464987 (22:41337846 G>A), RS1000555280 (22:41314984 A>G), RS1000574608 (22:41335065 A>C), RS1000716843 (22:41359559 G>A,C)

Disease associations

OMIM: gene MIM:618206 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

22 associations (top):

StudyTraitp-value
GCST004521_55Autism spectrum disorder or schizophrenia9.000000e-09
GCST004600_123Eosinophil percentage of white cells2.000000e-09
GCST004617_47Eosinophil percentage of granulocytes5.000000e-11
GCST004623_46Neutrophil percentage of granulocytes1.000000e-12
GCST004624_33Sum eosinophil basophil counts5.000000e-10
GCST004785_25Vitiligo3.000000e-15
GCST004946_20Schizophrenia1.000000e-12
GCST005232_52Neuroticism3.000000e-18
GCST006803_24Schizophrenia6.000000e-13
GCST007709_158General factor of neuroticism9.000000e-10
GCST007932_101Medication use (thyroid preparations)9.000000e-09
GCST010002_83Refractive error2.000000e-27
GCST010133_13Lamb consumption3.000000e-08
GCST010143_2Meat-related diet4.000000e-08
GCST010989_166Body size at age 108.000000e-09
GCST011124_12Caffeine consumption from tea2.000000e-10
GCST011702_1Smoking cessation1.000000e-08
GCST90002381_449Eosinophil count6.000000e-22
GCST90002382_513Eosinophil percentage of white cells2.000000e-21
GCST90002388_272Lymphocyte count2.000000e-29
GCST90020025_1735Waist-to-hip ratio adjusted for BMI2.000000e-08
GCST90020027_404Waist-hip index8.000000e-09

EFO canonical traits (13, from GWAS)

EFO IDTrait name
EFO:0007991eosinophil percentage of leukocytes
EFO:0007996eosinophil percentage of granulocytes
EFO:0007994neutrophil percentage of granulocytes
EFO:0004842eosinophil count
EFO:0005090basophil count
EFO:0007660neuroticism measurement
EFO:0009933Thyroid preparation use measurement
EFO:0008111diet measurement
EFO:0009819comparative body size at age 10, self-reported
EFO:0010091tea consumption measurement
EFO:0004319smoking cessation
EFO:0004587lymphocyte count
EFO:0007788BMI-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

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases methylation, increases expression, increases methylation3
trichostatin Aaffects expression, increases expression2
sodium arsenitedecreases expression, increases expression2
Valproic Acidaffects expression, decreases expression, increases methylation2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
dicrotophosincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
mono-(2-ethylhexyl)phthalateincreases abundance, increases methylation1
cobaltous chloridedecreases expression1
corosolic acidincreases expression1
abrineincreases expression1
(+)-JQ1 compounddecreases expression1
Arsenic Trioxideincreases expression1
Acetaminophendecreases expression1
Cadmiumincreases abundance, increases expression1
Caffeineincreases phosphorylation1
Diethylhexyl Phthalateincreases abundance, increases methylation1
Doxorubicindecreases expression1
Formaldehydeincreases expression1
Ivermectindecreases expression1
Ribonucleotidesaffects binding1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Triiodothyroninedecreases expression1
Aflatoxin B1increases methylation1
Antirheumatic Agentsincreases expression1
Cadmium Chlorideincreases abundance, increases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.