ZNF106

gene
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Also known as ZNF474SH3BP3

Summary

ZNF106 (zinc finger protein 106, HGNC:12886) is a protein-coding gene on chromosome 15q15.1, encoding Zinc finger protein 106 (Q9H2Y7). RNA-binding protein.

Enables RNA binding activity. Predicted to be involved in insulin receptor signaling pathway. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in cytosol and membrane.

Source: NCBI Gene 64397 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 288 total
  • MANE Select transcript: NM_001366845

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12886
Approved symbolZNF106
Namezinc finger protein 106
Location15q15.1
Locus typegene with protein product
StatusApproved
AliasesZNF474, SH3BP3
Ensembl geneENSG00000103994
Ensembl biotypeprotein_coding
OMIM603988
Entrez64397

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000263805, ENST00000564754, ENST00000565380, ENST00000565500, ENST00000565611, ENST00000565660, ENST00000565948, ENST00000567041, ENST00000567772, ENST00000568906, ENST00000569648, ENST00000570078

RefSeq mRNA: 12 — MANE Select: NM_001366845 NM_001284306, NM_001284307, NM_001366844, NM_001366845, NM_001366846, NM_001381993, NM_001381994, NM_001381995, NM_001381996, NM_001381997, NM_001381998, NM_022473

CCDS: CCDS32208, CCDS61602, CCDS61603, CCDS91986

Canonical transcript exons

ENST00000564754 — 22 exons

ExonStartEnd
ENSE000006790464241780542417951
ENSE000006790554242801842428134
ENSE000008841284243538442435518
ENSE000009311294243723242437377
ENSE000009311304243861242438667
ENSE000009311324244207342442414
ENSE000009311354244658942446658
ENSE000012320494243903342439813
ENSE000013428404241282342417360
ENSE000022153224247223642472321
ENSE000022747984246605342466114
ENSE000025885204245695842457158
ENSE000026088854249098042491141
ENSE000034725564242106142421132
ENSE000035104804242399842424060
ENSE000035970184242483442425025
ENSE000036299394242191742421988
ENSE000036386684242250142422620
ENSE000036414594244807242448705
ENSE000036795714244977142451954
ENSE000036971914244420242444262
ENSE000036982664244482742444981

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 99.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.2628 / max 1814.5796, expressed in 1796 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
14956315.05511776
14955814.4245889
1495521.5073664
1495610.5777263
2074860.5541244
1495620.5209281
1495590.241594
1495530.128637
1495600.127134
1495540.126037

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skeletal muscle tissue of rectus abdominisUBERON:000451199.47gold quality
diaphragmUBERON:000110399.41gold quality
gluteal muscleUBERON:000200099.40gold quality
left ventricle myocardiumUBERON:000656699.39gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.37gold quality
biceps brachiiUBERON:000150799.36gold quality
vastus lateralisUBERON:000137999.30gold quality
quadriceps femorisUBERON:000137799.24gold quality
body of tongueUBERON:001187699.24gold quality
skeletal muscle tissueUBERON:000113499.11gold quality
deltoidUBERON:000147699.11gold quality
heart right ventricleUBERON:000208099.04gold quality
tibialis anteriorUBERON:000138598.90gold quality
triceps brachiiUBERON:000150998.89gold quality
myocardiumUBERON:000234998.88gold quality
muscle organUBERON:000163098.73gold quality
skeletal muscle organUBERON:001489298.73gold quality
cardiac muscle of right atriumUBERON:000337998.57gold quality
gastrocnemiusUBERON:000138898.55gold quality
muscle of legUBERON:000138398.53gold quality
muscle tissueUBERON:000238598.39gold quality
hindlimb stylopod muscleUBERON:000425298.22gold quality
tongueUBERON:000172397.59gold quality
cardiac ventricleUBERON:000208297.17gold quality
heart left ventricleUBERON:000208497.11gold quality
choroid plexus epitheliumUBERON:000391197.00gold quality
vena cavaUBERON:000408796.79gold quality
calcaneal tendonUBERON:000370196.50gold quality
superior surface of tongueUBERON:000737196.46gold quality
dorsal motor nucleus of vagus nerveUBERON:000287096.16gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-135922yes485.78
E-ANND-3yes19.12
E-MTAB-7249no7502.78
E-ENAD-20no1891.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

185 targeting ZNF106, 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-188-3P100.0068.761240
HSA-MIR-8485100.0077.574731
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-453199.9969.703181
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-318599.9968.121959
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-548N99.9871.944170
HSA-MIR-480399.9871.993117
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-314899.9775.066478
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-570-3P99.9672.414910
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-314399.9371.963104
HSA-MIR-548AE-3P99.9372.664867

Literature-anchored findings (GeneRIF, showing 2)

  • Study identified ZFP106 as a novel substrate for CBP-mediated acetylation, and showed that the fully disordered isolated ID3 in CREBBP transiently interacts with an IDR of ZFP106 in a fashion that both IDR regions are maintained. (PMID:28680062)
  • Whole-exome Sequencing Identifies SLC52A1 and ZNF106 Variants as Novel Genetic Risk Factors for (Early) Multiple-organ Failure in Acute Pancreatitis. (PMID:33427755)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioznf106aENSDARG00000016651
danio_rerioznf106bENSDARG00000091947
mus_musculusZfp106ENSMUSG00000027288
rattus_norvegicusZfp106ENSRNOG00000052583

Protein

Protein identifiers

Zinc finger protein 106Q9H2Y7 (reviewed: Q9H2Y7)

Alternative names: Zinc finger protein 474

All UniProt accessions (8): A0A0C4DGM5, Q9H2Y7, H3BNJ4, H3BNX5, H3BRD4, H3BS99, H3BSS6, U3KQH7

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein. Specifically binds to 5’-GGGGCC-3’ sequence repeats in RNA. Essential for maintenance of peripheral motor neuron and skeletal muscle function. Required for normal expression and/or alternative splicing of a number of genes in spinal cord and skeletal muscle, including the neurite outgrowth inhibitor RTN4. Also contributes to normal mitochondrial respiratory function in motor neurons, via an unknown mechanism.

Subunit / interactions. Interacts with KNOP1. Interacts with TARDBP and NUP107. Interacts (via N-terminus) with RBM39. Interacts with the SH3 domains of FYN and GRB2.

Subcellular location. Nucleus. Nucleolus. Nucleus speckle.

Post-translational modifications. Phosphorylated by FYN in vitro.

Isoforms (2)

UniProt IDNamesCanonical?
Q9H2Y7-11yes
Q9H2Y7-22

RefSeq proteins (12): NP_001271235, NP_001271236, NP_001353773, NP_001353774, NP_001353775, NP_001368922, NP_001368923, NP_001368924, NP_001368925, NP_001368926, NP_001368927, NP_071918 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR013087Znf_C2H2_typeDomain
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR042622Znf106Family

Pfam: PF00400

UniProt features (120 total): cross-link 44, modified residue 22, compositionally biased region 21, region of interest 12, repeat 6, sequence conflict 6, sequence variant 4, splice variant 2, zinc finger region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H2Y7-F144.820.11

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 (66): 1454, 1486, 1504, 1585, 1737, 1864, 6, 37, 422, 590, 641, 661, 859, 861, 864, 893, 937, 1021, 1025, 1026 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 230 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, HORIUCHI_WTAP_TARGETS_DN, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_CELLULAR_RESPONSE_TO_INSULIN_STIMULUS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN, MARTINEZ_RB1_TARGETS_UP, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS, GOBP_RESPONSE_TO_INSULIN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, MODULE_256, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_CELLULAR_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_HORMONE

GO Biological Process (1): insulin receptor signaling pathway (GO:0008286)

GO Molecular Function (4): RNA binding (GO:0003723), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleolus (GO:0005730), cytosol (GO:0005829), membrane (GO:0016020), nuclear speck (GO:0016607), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cell surface receptor protein tyrosine kinase signaling pathway1
cellular response to insulin stimulus1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1
nuclear lumen1
intracellular membraneless organelle1
cytoplasm1
nuclear ribonucleoprotein granule1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1314 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF106ZNF91Q05481815
ZNF106KNOP1Q1ED39643
ZNF106PURAQ00577588
ZNF106ADARB2Q9NS39574
ZNF106ALYREFQ86V81562
ZNF106TARDBPQ13148536
ZNF106ZDHHC22Q8N966513
ZNF106C1orf159Q96HA4507
ZNF106DNHD1Q96M86473
ZNF106RANGAP1P46060469
ZNF106PTCD2Q8WV60459
ZNF106NUCLEOLINP19338455
ZNF106ZNHIT2Q9UHR6455
ZNF106PPFIA1Q13136447
ZNF106FRMD8Q9BZ67447
ZNF106TOPORSQ9NS56447

IntAct

77 interactions, top by confidence:

ABTypeScore
CSNK2A2EIF3Jpsi-mi:“MI:0914”(association)0.790
SMARCD1ARID1Apsi-mi:“MI:0914”(association)0.790
CSNK2BNMT2psi-mi:“MI:0914”(association)0.660
STAMBPL1PIK3C2Apsi-mi:“MI:0914”(association)0.640
CSNK2BRPS6KA4psi-mi:“MI:0914”(association)0.640
NEURL4APBB1psi-mi:“MI:0914”(association)0.530
KLHL40CBX4psi-mi:“MI:0914”(association)0.530
KNOP1DHX15psi-mi:“MI:0914”(association)0.530
CLEC11AVWA8psi-mi:“MI:0914”(association)0.530
FHL2CNOT1psi-mi:“MI:0914”(association)0.530
DDX21MED19psi-mi:“MI:2364”(proximity)0.480
Cep170WDR62psi-mi:“MI:0915”(physical association)0.400
PCNAZNF106psi-mi:“MI:0915”(physical association)0.370
ZNF106CFAP418psi-mi:“MI:0915”(physical association)0.370
ZNF106SKILpsi-mi:“MI:0915”(physical association)0.370
Cep170NEURL4psi-mi:“MI:0914”(association)0.350
MATR3BCLAF3psi-mi:“MI:0914”(association)0.350
GTSE1HIP1psi-mi:“MI:0914”(association)0.350
Kif18aWASLpsi-mi:“MI:0914”(association)0.350
Uso1GOLGA2psi-mi:“MI:0914”(association)0.350
CAPZA2PLEKHG3psi-mi:“MI:0914”(association)0.350
EXOSC9MPHOSPH6psi-mi:“MI:0914”(association)0.350
KIF21ANCOA4psi-mi:“MI:0914”(association)0.350
PPP1CBPLEKHG3psi-mi:“MI:0914”(association)0.350

BioGRID (106): ZNF106 (Affinity Capture-RNA), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS), ZNF106 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WXM9, A0A2K1JJ00, A0JM83, A4IGL8, E1BC15, E9Q5F9, O14513, O35923, O60673, O88491, P46013, P97929, Q14B71, Q28DZ0, Q29RT4, Q3MHH3, Q3TNU4, Q3ZBP0, Q4QY64, Q4V7J0, Q5DTT3, Q5E9A0, Q5F2C3, Q5RD08, Q5VWN6, Q5VYV7, Q61493, Q69YH5, Q6NS59, Q703I1, Q80U59, Q86XD8, Q8IXS0, Q8IYL3, Q8L7I1, Q8N7Z5, Q8NFU7, Q8TEP8, Q92628, Q96BU1

Diamond homologs: A4RDD7, A6ZPA6, A7EF03, A7THX0, B3LJT5, B4HSL3, B4QHG6, B8P4B0, B8PD53, B9WD30, C4YPI7, C5DF48, C5DY07, C5FP68, C5MJE8, C7GWC1, C8ZH19, D3TLL6, D4AM37, D4D8P3, O00628, P39946, P97865, Q54WA3, Q5A7Q3, Q5A7Q6, Q6CJ50, Q6CU55, Q6DFC6, Q6FT96, Q6FWT9, Q759U7, Q7KNS3, Q7RXH4, Q8IWA0, Q8R537, Q8RXA7, Q9H2Y7, A6ZQL5, B0WC36

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 99 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
SARS-CoV-1 targets host intracellular signalling and regulatory pathways656.0×3e-07
Activation of BAD and translocation to mitochondria552.9×3e-06
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex546.6×4e-06
Activation of BH3-only proteins534.5×1e-05
RHO GTPases activate PKNs626.4×6e-06
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known520.9×1e-04
Intrinsic Pathway for Apoptosis520.3×1e-04
SARS-CoV-1-host interactions819.5×2e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance239
Likely benign22
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2654 predictions. Top by Δscore:

VariantEffectΔscore
15:42417280:T:TAdonor_gain1.0000
15:42417280:TCCCA:Tdonor_gain1.0000
15:42417281:C:Adonor_gain1.0000
15:42417304:T:TAdonor_gain1.0000
15:42417819:T:Adonor_gain1.0000
15:42417947:TGCCA:Tacceptor_gain1.0000
15:42417949:CCA:Cacceptor_gain1.0000
15:42417950:CA:Cacceptor_gain1.0000
15:42417950:CAC:Cacceptor_gain1.0000
15:42417952:C:CCacceptor_gain1.0000
15:42421055:CCTTA:Cdonor_loss1.0000
15:42421056:CTT:Cdonor_loss1.0000
15:42421057:TTACC:Tdonor_loss1.0000
15:42421058:T:TAdonor_loss1.0000
15:42421059:A:ATdonor_loss1.0000
15:42421059:AC:Adonor_gain1.0000
15:42421060:C:CAdonor_loss1.0000
15:42421060:CC:Cdonor_gain1.0000
15:42421060:CCCAA:Cdonor_gain1.0000
15:42421132:TCT:Tacceptor_loss1.0000
15:42421133:C:CAacceptor_loss1.0000
15:42421909:ACACT:Adonor_loss1.0000
15:42421912:CTCA:Cdonor_loss1.0000
15:42421913:TCA:Tdonor_loss1.0000
15:42421914:C:CGdonor_loss1.0000
15:42421915:A:ACdonor_gain1.0000
15:42421915:A:Cdonor_loss1.0000
15:42421916:C:CCdonor_gain1.0000
15:42421916:CCATG:Cdonor_gain1.0000
15:42421984:TGAGA:Tacceptor_gain1.0000

AlphaMissense

12593 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:42417858:A:GC1848R1.000
15:42421064:A:CC1815W1.000
15:42421066:A:GC1815R1.000
15:42421122:C:TG1796D1.000
15:42422517:C:GR1763P1.000
15:42422520:A:TV1762D1.000
15:42422529:T:AD1759V1.000
15:42422534:G:CC1757W1.000
15:42422547:A:CM1753R1.000
15:42422599:A:CY1736D1.000
15:42422616:C:AG1730V1.000
15:42422616:C:TG1730D1.000
15:42424008:T:GH1725P1.000
15:42424009:G:CH1725D1.000
15:42424011:G:TA1724D1.000
15:42424012:C:GA1724P1.000
15:42424017:A:TV1722D1.000
15:42424021:A:GS1721P1.000
15:42424026:T:AD1719V1.000
15:42424026:T:GD1719A1.000
15:42424027:C:AD1719Y1.000
15:42424027:C:GD1719H1.000
15:42424035:C:TG1716D1.000
15:42424036:C:GG1716R1.000
15:42424037:A:CS1715R1.000
15:42424037:A:TS1715R1.000
15:42424039:T:GS1715R1.000
15:42424041:A:GF1714S1.000
15:42424044:A:TV1713E1.000
15:42424047:A:GL1712P1.000

dbSNP variants (sampled 300 via entrez): RS1000078351 (15:42482195 C>T), RS1000123021 (15:42486642 G>A), RS1000179648 (15:42434155 T>A), RS1000196673 (15:42437103 T>C), RS1000247504 (15:42437392 T>C), RS1000262218 (15:42445218 G>A), RS1000272601 (15:42479232 G>A), RS1000301520 (15:42438393 C>T), RS1000392045 (15:42431066 T>C), RS1000438414 (15:42438086 G>A), RS1000478445 (15:42473740 A>G), RS1000500105 (15:42488038 G>T), RS1000502293 (15:42458657 G>A), RS1000594683 (15:42446937 T>A), RS1000595042 (15:42444047 G>C)

Disease associations

OMIM: gene MIM:603988 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST010083_5Hemoglobin levels1.000000e-10
GCST010173_12Triglyceride levels7.000000e-24
GCST90002384_377Hemoglobin4.000000e-09
GCST90002397_254Mean spheric corpuscular volume3.000000e-09
GCST90002403_479Red blood cell count3.000000e-14

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004509hemoglobin measurement
EFO:0004530triglyceride measurement
EFO:0004305erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophendecreases expression, increases expression2
FR900359affects phosphorylation1
TAK-243increases sumoylation1
dicrotophosincreases expression1
bisphenol Aincreases expression1
arseniteaffects binding, decreases reaction1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
nickel chloridedecreases expression1
manganese chloridedecreases expression, increases abundance, affects cotreatment1
aflatoxin B2increases methylation1
coumarindecreases phosphorylation1
beta-methylcholineaffects expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Caffeinedecreases phosphorylation1
Carbamazepineaffects expression1
Doxorubicindecreases expression1
Leadaffects expression1
Manganesedecreases expression, increases abundance, affects cotreatment1
Ribonucleotidesaffects binding1
Testosteronedecreases expression1
Thiramincreases expression1
Tretinoinincreases expression1
Valproic Acidaffects expression1
Aflatoxin B1decreases methylation1
Cadmium Chlorideincreases expression1
Acrylamideincreases 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.