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ZMAT2

gene
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Also known as FLJ31121hSNU23Snu23

Summary

ZMAT2 (zinc finger matrin-type 2, HGNC:26433) is a protein-coding gene on chromosome 5q31.3, encoding Zinc finger matrin-type protein 2 (Q96NC0). Involved in pre-mRNA splicing as a component of the spliceosome. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

Predicted to enable DNA binding activity and zinc ion binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleus. Part of U2-type precatalytic spliceosome.

Source: NCBI Gene 153527 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): congenital radioulnar synostosis (Limited, GenCC)
  • GWAS associations: 6
  • Clinical variants (ClinVar): 17 total
  • Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_144723

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26433
Approved symbolZMAT2
Namezinc finger matrin-type 2
Location5q31.3
Locus typegene with protein product
StatusApproved
AliasesFLJ31121, hSNU23, Snu23
Ensembl geneENSG00000146007
Ensembl biotypeprotein_coding
OMIM619930
Entrez153527

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 nonsense_mediated_decay

ENST00000274712, ENST00000506644, ENST00000519913, ENST00000924923, ENST00000924924

RefSeq mRNA: 1 — MANE Select: NM_144723 NM_144723

CCDS: CCDS4239

Canonical transcript exons

ENST00000274712 — 6 exons

ExonStartEnd
ENSE00001085718140705613140706686
ENSE00001127540140700447140700478
ENSE00003299003140703918140703991
ENSE00003463244140700819140700912
ENSE00003542009140704426140704571
ENSE00003569063140702006140702129

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 98.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 65.8752 / max 2181.7494, expressed in 1825 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
5893365.87521825

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534398.39gold quality
monocyteCL:000057697.98gold quality
islet of LangerhansUBERON:000000697.95gold quality
embryoUBERON:000092297.92gold quality
ganglionic eminenceUBERON:000402397.92gold quality
leukocyteCL:000073897.91gold quality
prefrontal cortexUBERON:000045197.86gold quality
nucleus accumbensUBERON:000188297.47gold quality
caudate nucleusUBERON:000187397.45gold quality
putamenUBERON:000187497.34gold quality
anterior cingulate cortexUBERON:000983597.33gold quality
colonic epitheliumUBERON:000039797.16gold quality
gastrocnemiusUBERON:000138897.05gold quality
Brodmann (1909) area 9UBERON:001354097.01gold quality
ileal mucosaUBERON:000033196.94gold quality
muscle of legUBERON:000138396.93gold quality
frontal cortexUBERON:000187096.84gold quality
right frontal lobeUBERON:000281096.84gold quality
descending thoracic aortaUBERON:000234596.79gold quality
neocortexUBERON:000195096.77gold quality
dorsolateral prefrontal cortexUBERON:000983496.72gold quality
smooth muscle tissueUBERON:000113596.67gold quality
tibialis anteriorUBERON:000138596.64gold quality
mucosa of transverse colonUBERON:000499196.55gold quality
amygdalaUBERON:000187696.46gold quality
granulocyteCL:000009496.43gold quality
rectumUBERON:000105296.38gold quality
ventricular zoneUBERON:000305396.37gold quality
esophagus mucosaUBERON:000246996.28gold quality
thoracic aortaUBERON:000151596.25gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

85 targeting ZMAT2, 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-4673100.0066.641490
HSA-MIR-8485100.0077.574731
HSA-MIR-4692100.0067.322066
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3646100.0073.565283
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-451499.9967.101870
HSA-MIR-150-5P99.9966.691976
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-50799.9770.111915
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-55799.9670.011640
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-335-3P99.9373.364958
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-129-5P99.8870.263273
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-6875-3P99.8270.262983

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • Zmat2 in mammals: conservation and diversification among genes and Pseudogenes. (PMID:32005145)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriozmat2ENSDARG00000004956
mus_musculusZmat2ENSMUSG00000001383
rattus_norvegicusZmat2ENSRNOG00000072190
drosophila_melanogasterCG11586FBGN0035520

Paralogs (9): ZNF346 (ENSG00000113761), ZNF385B (ENSG00000144331), ZNF385D (ENSG00000151789), ZNF385A (ENSG00000161642), ZMAT4 (ENSG00000165061), ZMAT1 (ENSG00000166432), KRCC1 (ENSG00000172086), ZMAT3 (ENSG00000172667), ZNF385C (ENSG00000187595)

Protein

Protein identifiers

Zinc finger matrin-type protein 2 — Q96NC0 (reviewed: Q96NC0)

All UniProt accessions (3): Q96NC0, R4GMX9, R4GNG8

UniProt curated annotations — full annotation on UniProt →

Function. Involved in pre-mRNA splicing as a component of the spliceosome.

Subunit / interactions. Component of the spliceosome B complex.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_653324* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003604Matrin/U1-like-C_Znf_C2H2Domain
IPR022755Znf_C2H2_jazDomain
IPR036236Znf_C2H2_sfHomologous_superfamily
IPR040107Snu23Family

Pfam: PF12171

UniProt features (24 total): cross-link 10, helix 3, turn 2, strand 2, region of interest 2, initiator methionine 1, chain 1, zinc finger region 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

13 structures.

PDBMethodResolution (Å)
8H6KELECTRON MICROSCOPY2.7
8Q7NELECTRON MICROSCOPY3.1
8QPEELECTRON MICROSCOPY3.1
9R3DELECTRON MICROSCOPY3.12
6AHDELECTRON MICROSCOPY3.8
7ABFELECTRON MICROSCOPY3.9
8QZSELECTRON MICROSCOPY4.1
7AAVELECTRON MICROSCOPY4.2
5O9ZELECTRON MICROSCOPY4.5
8QO9ELECTRON MICROSCOPY5.29
7ABGELECTRON MICROSCOPY7.8
7ABIELECTRON MICROSCOPY8
9R8VELECTRON MICROSCOPY8.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96NC0-F172.370.03

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 (11): 45, 55, 61, 64, 70, 102, 123, 2, 8, 36, 39

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway

MSigDB gene sets: 126 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, IRF1_Q6, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, REACTOME_METABOLISM_OF_RNA, GOCC_U2_TYPE_SPLICEOSOMAL_COMPLEX, GOCC_PRECATALYTIC_SPLICEOSOME, chr5q31, GOCC_SPLICEOSOMAL_TRI_SNRNP_COMPLEX, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, TARTE_PLASMA_CELL_VS_PLASMABLAST_DN, KEGG_SPLICEOSOME

GO Biological Process (3): mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (5): DNA binding (GO:0003677), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), spliceosomal complex (GO:0005681)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
mRNA Splicing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
binding2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile1
mRNA processing1
mRNA metabolic process1
nucleic acid binding1
transition metal ion binding1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
U5 snRNP1
U4/U6 snRNP1
spliceosomal tri-snRNP complex1
U2-type spliceosomal complex1
U1 snRNP1
U2 snRNP1
U4/U6 x U5 tri-snRNP complex1
precatalytic spliceosome1
nuclear protein-containing complex1
ribonucleoprotein complex1

Protein interactions and networks

STRING

1290 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZMAT2MFAP1P55081905
ZMAT2PRPF38AQ8NAV1827
ZMAT2SMU1Q2TAY7826
ZMAT2SART1O43290783
ZMAT2WBP4O75554777
ZMAT2SNRNP200O75643626
ZMAT2DDX23Q9BUQ8604
ZMAT2PRPF6O94906594
ZMAT2PRPF31Q8WWY3578
ZMAT2PRP4KQ13523535
ZMAT2SF3A3Q12874531
ZMAT2TXNL4AP83876530
ZMAT2RBM42Q9BTD8523
ZMAT2SF3A2Q15428517
ZMAT2PPIHO43447502

IntAct

222 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:0914”(association)0.900
FXR2ZMAT2psi-mi:“MI:0915”(physical association)0.720
GOLGA2ZMAT2psi-mi:“MI:0915”(physical association)0.720
TRAF2ZMAT2psi-mi:“MI:0915”(physical association)0.720
ZMAT2GOLGA2psi-mi:“MI:0915”(physical association)0.720
ZMAT2TRAF2psi-mi:“MI:0915”(physical association)0.720
HTTZMAT2psi-mi:“MI:0915”(physical association)0.700

BioGRID (133): ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid), ZMAT2 (Two-hybrid)

ESM2 similar proteins: A1C8E1, A3LU29, B0JZ89, B2W2Y7, O43082, O45766, O94389, O95926, P0CM66, P0CM67, P53188, Q0C7E6, Q0UVD1, Q0V389, Q1E554, Q28HN4, Q28IN9, Q28XK6, Q2HDR6, Q2TVY9, Q3B748, Q4I5Z5, Q568A0, Q59WI7, Q5B020, Q68EY7, Q6BIC4, Q6BWR0, Q6C1V5, Q6CNQ3, Q6DD17, Q6DGP2, Q6DKE6, Q6FVC7, Q6NVR5, Q6PHE8, Q752U2, Q7SDA6, Q7ZY35, Q8AVQ6

Diamond homologs: P34670, Q96NC0, Q9CPW7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance4
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

556 predictions. Top by Δscore:

VariantEffectΔscore
5:140700474:GCGGG:Gdonor_gain1.0000
5:140700814:CACAG:Cacceptor_loss1.0000
5:140700815:ACAG:Aacceptor_loss1.0000
5:140700816:CAGAC:Cacceptor_loss1.0000
5:140700817:A:AGacceptor_gain1.0000
5:140700817:AGA:Aacceptor_loss1.0000
5:140700818:G:GAacceptor_gain1.0000
5:140700818:GA:Gacceptor_gain1.0000
5:140700818:GACA:Gacceptor_gain1.0000
5:140700818:GACAA:Gacceptor_gain1.0000
5:140700891:G:GTdonor_gain1.0000
5:140700909:GATG:Gdonor_gain1.0000
5:140700913:GTG:Gdonor_loss1.0000
5:140700914:T:Adonor_loss1.0000
5:140701994:ATTAT:Aacceptor_gain1.0000
5:140701997:A:AGacceptor_gain1.0000
5:140701997:AT:Aacceptor_gain1.0000
5:140701998:T:Gacceptor_gain1.0000
5:140701998:T:TAacceptor_gain1.0000
5:140702001:TTCAG:Tacceptor_loss1.0000
5:140702002:TCAG:Tacceptor_loss1.0000
5:140702003:CAGG:Cacceptor_loss1.0000
5:140702004:A:AGacceptor_gain1.0000
5:140702004:AG:Aacceptor_gain1.0000
5:140702005:G:GTacceptor_gain1.0000
5:140702005:GG:Gacceptor_gain1.0000
5:140702005:GGA:Gacceptor_gain1.0000
5:140702005:GGAA:Gacceptor_gain1.0000
5:140702005:GGAAA:Gacceptor_gain1.0000
5:140702082:G:GTdonor_gain1.0000

AlphaMissense

1341 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:140700846:T:AW16R1.000
5:140700846:T:CW16R1.000
5:140700848:G:CW16C1.000
5:140700848:G:TW16C1.000
5:140702039:T:CL49S1.000
5:140702047:A:GR52G1.000
5:140702048:G:CR52T1.000
5:140702048:G:TR52M1.000
5:140702049:G:CR52S1.000
5:140702049:G:TR52S1.000
5:140702066:T:CL58S1.000
5:140702081:G:AG63E1.000
5:140702081:G:TG63V1.000
5:140702093:T:AV67D1.000
5:140702096:T:AI68N1.000
5:140702096:T:GI68S1.000
5:140702125:G:AG78R1.000
5:140702125:G:CG78R1.000
5:140702126:G:AG78E1.000
5:140702128:G:AG79R1.000
5:140702128:G:CG79R1.000
5:140702129:G:AG79E1.000
5:140702129:G:TG79V1.000
5:140703925:T:AC82S1.000
5:140703925:T:CC82R1.000
5:140703925:T:GC82G1.000
5:140703926:G:AC82Y1.000
5:140703926:G:CC82S1.000
5:140703926:G:TC82F1.000
5:140703927:C:GC82W1.000

dbSNP variants (sampled 300 via entrez): RS1000368237 (5:140705272 C>A), RS1000440110 (5:140704886 A>G), RS1000909244 (5:140701953 T>A,G), RS1000984694 (5:140699872 T>C), RS1001353598 (5:140700190 G>A,T), RS1002329302 (5:140706243 G>A,C), RS1002387717 (5:140698926 C>A,T), RS1002481235 (5:140699446 A>G), RS1003213047 (5:140704145 A>G), RS1003256461 (5:140704720 G>A,C), RS1003328189 (5:140703685 ACT>A), RS1003736420 (5:140704183 T>A), RS1004805818 (5:140701779 T>C), RS1005111137 (5:140701342 G>A), RS1005501067 (5:140700710 C>G,T)

Disease associations

OMIM: gene MIM:619930 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
congenital radioulnar synostosisLimitedAutosomal dominant

Mondo (1): congenital radioulnar synostosis (MONDO:0017985)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST004946_157Schizophrenia2.000000e-08
GCST006041_22Major depressive disorder9.000000e-08
GCST006624_37Systolic blood pressure8.000000e-15
GCST006803_54Schizophrenia8.000000e-07
GCST010002_39Refractive error2.000000e-14
GCST010146_22Serum immune biomarker levels7.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0006335systolic blood pressure
EFO:0004872inflammatory biomarker measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C562408Radioulnar Synostosis (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Idecreases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Adecreases expression1
beta-lapachoneincreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
yessotoxindecreases expression1
CGP 52608affects binding, increases reaction1
PP242increases expression1
Norethindrone Acetateaffects cotreatment, increases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Benzo(a)pyrenedecreases expression1
Copperaffects binding, decreases expression1
Disulfiramaffects binding, decreases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, increases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Aflatoxin B1increases methylation1
Volatile Organic Compoundsaffects cotreatment, increases oxidation1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot