ZMAT5

Summary

ZMAT5 (zinc finger matrin-type 5, HGNC:28046) is a protein-coding gene on chromosome 22q12.2, encoding Zinc finger matrin-type protein 5 (Q9UDW3). It is a common-essential gene (DepMap: required in 98.0% of cancer cell lines).

Predicted to enable zinc ion binding activity. Predicted to be involved in RNA splicing. Located in nucleoplasm. Part of U12-type spliceosomal complex.

Source: NCBI Gene 55954 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 24 total
• Cancer dependency (DepMap): dependent in 98.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_001003692

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28046
Approved symbol	ZMAT5
Name	zinc finger matrin-type 5
Location	22q12.2
Locus type	gene with protein product
Status	Approved
Aliases	SNRNP20
Ensembl gene	ENSG00000100319
Ensembl biotype	protein_coding
OMIM	619741
Entrez	55954

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 27 protein_coding, 1 retained_intron

ENST00000344318, ENST00000489010, ENST00000890523, ENST00000890526, ENST00000890529, ENST00000890530, ENST00000890531, ENST00000890533, ENST00000890536, ENST00000890540, ENST00000890542, ENST00000890544, ENST00000890548, ENST00000890551, ENST00000890552, ENST00000890554, ENST00000890556, ENST00000890558, ENST00000922634, ENST00000922635, ENST00000922636, ENST00000922637, ENST00000922638, ENST00000922639, ENST00000952497, ENST00000952498, ENST00000952499, ENST00000952500

RefSeq mRNA: 3 — MANE Select: NM_001003692 NM_001003692, NM_001318129, NM_019103

CCDS: CCDS13868

Canonical transcript exons

ENST00000344318 — 6 exons

Exon	Start	End
ENSE00000652123	29738330	29738441
ENSE00000879757	29740650	29740730
ENSE00000879758	29742418	29742480
ENSE00001048317	29766872	29767007
ENSE00001326651	29748418	29748571
ENSE00001935382	29730956	29731354

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 91.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.1297 / max 67.8986, expressed in 1802 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193551	11.1824	1799
193550	0.5291	316
193552	0.3346	128
193548	0.0595	10
193549	0.0242	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	91.79	gold quality
apex of heart	UBERON:0002098	90.96	gold quality
granulocyte	CL:0000094	89.63	gold quality
gastrocnemius	UBERON:0001388	89.20	gold quality
muscle of leg	UBERON:0001383	88.83	gold quality
right adrenal gland	UBERON:0001233	88.41	gold quality
left adrenal gland cortex	UBERON:0035825	87.92	gold quality
left adrenal gland	UBERON:0001234	87.87	gold quality
right adrenal gland cortex	UBERON:0035827	87.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	87.68	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.41	gold quality
monocyte	CL:0000576	86.72	gold quality
right uterine tube	UBERON:0001302	86.55	gold quality
leukocyte	CL:0000738	86.50	gold quality
mononuclear cell	CL:0000842	86.38	gold quality
right atrium auricular region	UBERON:0006631	86.27	gold quality
right lobe of liver	UBERON:0001114	86.21	gold quality
lower esophagus	UBERON:0013473	86.04	gold quality
lower esophagus muscularis layer	UBERON:0035833	86.04	gold quality
stromal cell of endometrium	CL:0002255	86.01	gold quality
anterior cingulate cortex	UBERON:0009835	85.96	gold quality
thoracic aorta	UBERON:0001515	85.92	gold quality
ascending aorta	UBERON:0001496	85.88	gold quality
body of stomach	UBERON:0001161	85.86	gold quality
cingulate cortex	UBERON:0003027	85.82	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.61	gold quality
adrenal cortex	UBERON:0001235	85.56	gold quality
descending thoracic aorta	UBERON:0002345	85.46	gold quality
tibial nerve	UBERON:0001323	85.42	gold quality
ganglionic eminence	UBERON:0004023	85.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-3929	yes	433.27
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting ZMAT5, 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-340-5P	100.00	72.50	4437
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-516A-3P	99.46	67.96	1378
HSA-MIR-516B-3P	99.46	67.96	1378
HSA-MIR-7162-5P	99.46	68.08	1368
HSA-MIR-328-5P	99.08	64.65	1000
HSA-MIR-6885-5P	98.71	64.33	902
HSA-MIR-3136-5P	98.53	67.68	793
HSA-MIR-4439	98.53	67.53	793
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-134-5P	97.11	66.52	976
HSA-MIR-3118	97.11	66.58	984
HSA-MIR-6857-3P	96.70	65.43	915
HSA-MIR-6823-3P	95.45	66.14	704
HSA-MIR-2114-3P	95.45	66.11	579
HSA-MIR-4513	95.04	67.06	727
HSA-MIR-6855-3P	95.04	66.57	725

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.0% of screened cell lines, common-essential.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	zmat5	ENSDARG00000035434
mus_musculus	Zmat5	ENSMUSG00000009076
rattus_norvegicus	Zmat5	ENSRNOG00000007849
drosophila_melanogaster	CG31922	FBGN0051922

Protein

Protein identifiers

Zinc finger matrin-type protein 5 — Q9UDW3 (reviewed: Q9UDW3)

Alternative names: U11/U12 small nuclear ribonucleoprotein 20 kDa protein

All UniProt accessions (1): Q9UDW3

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Not found in the major spliceosome.

Subcellular location. Nucleus.

RefSeq proteins (3): NP_001003692, NP_001305058, NP_061976 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR013085	U1-CZ_Znf_C2H2	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR036855	Znf_CCCH_sf	Homologous_superfamily

Pfam: PF00642, PF06220

UniProt features (8 total): strand 2, helix 2, chain 1, zinc finger region 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
9GCL	ELECTRON MICROSCOPY	3
9GC0	ELECTRON MICROSCOPY	3.2
8Y6O	ELECTRON MICROSCOPY	3.38
8R7N	ELECTRON MICROSCOPY	3.4
9GBW	ELECTRON MICROSCOPY	3.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UDW3-F1	84.45	0.52

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway

MSigDB gene sets: 82 (showing top): RICKMAN_METASTASIS_DN, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, TGANTCA_AP1_C, REACTOME_MRNA_SPLICING, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, GOCC_PRECATALYTIC_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOCC_U12_TYPE_SPLICEOSOMAL_COMPLEX, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, LU_EZH2_TARGETS_UP

GO Biological Process (2): mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleoplasm (GO:0005654), U12-type spliceosomal complex (GO:0005689), nucleus (GO:0005634), spliceosomal complex (GO:0005681)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
mRNA Splicing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
mRNA metabolic process	1
transition metal ion binding	1
binding	1
cation binding	1
nuclear lumen	1
cellular anatomical structure	1
spliceosomal complex	1
intracellular membrane-bounded organelle	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1

Protein interactions and networks

STRING

1614 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMAT5	SNRNP25	Q9BV90	778
ZMAT5	SNRNP48	Q6IEG0	709
ZMAT5	SNRNP35	Q16560	664
ZMAT5	ZCRB1	Q8TBF4	635
ZMAT5	RNPC3	Q96LT9	542
ZMAT5	TMEM186	Q96B77	483
ZMAT5	SNRPF	P62306	466
ZMAT5	DDX42	Q86XP3	456
ZMAT5	SNX29	Q8TEQ0	455
ZMAT5	FBXO21	O94952	451
ZMAT5	ZNF277	Q9NRM2	449
ZMAT5	SNRPD2	P43330	444
ZMAT5	ASCC2	Q9H1I8	442
ZMAT5	LSM4	Q9Y4Z0	441
ZMAT5	CARD8	Q9Y2G2	433

IntAct

73 interactions, top by confidence:

A	B	Type	Score
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
ZCRB1	SF3B1	psi-mi:“MI:0914”(association)	0.640
TCHP	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
ZNF417	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
FANCL	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
RBPMS2	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
HOXC8	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
GEM	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
ARMC7	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
SMARCD1	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
AIRIM	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
BYSL	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
VPS37C	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
CREB5	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
GPANK1	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
MLH1	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
PIH1D2	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
CCDC120	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
PLEKHA7	ZMAT5	psi-mi:“MI:0915”(physical association)	0.560
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
ZMAT5	DENND4B	psi-mi:“MI:0914”(association)	0.530
SNRPF	SNRPGP15	psi-mi:“MI:0914”(association)	0.530

BioGRID (79): ZMAT5 (Affinity Capture-MS), ZMAT5 (Affinity Capture-MS), ZMAT5 (Affinity Capture-MS), DENND4B (Affinity Capture-MS), ZMAT5 (Affinity Capture-MS), ZCRB1 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), ZMAT5 (Affinity Capture-MS), RNPC3 (Affinity Capture-MS), ZMAT5 (Affinity Capture-MS), SNRNP48 (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), PSMG4 (Affinity Capture-MS), PSMG3 (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS)

ESM2 similar proteins: A6QQJ8, A9JTG5, B0F0H3, D3YY23, E0X9N4, E6ZIJ1, E9QAM5, O14976, P39428, P97874, Q13064, Q13077, Q17RB8, Q1L5Z9, Q1L8G6, Q1LXR6, Q2TA39, Q4R5T4, Q5FWT8, Q5NU13, Q5R7G8, Q5REG4, Q5T124, Q5ZA07, Q60764, Q6AXL8, Q6GLD9, Q6IDS6, Q6NZR5, Q76LS9, Q80V91, Q8IZP6, Q8K1S6, Q8N5J2, Q8N9I9, Q8R512, Q8WWL2, Q99KY4, Q9CQR5, Q9D572

Diamond homologs: O48772, Q0JP11, Q2TA39, Q54YA5, Q6AXL8, Q6NPN3, Q9CQR5, Q9SQU4, Q9UDW3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 36 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:

Pathway	Partners	Fold	FDR
mRNA Splicing - Minor Pathway	6	58.4×	4e-08
snRNP Assembly	5	46.0×	7e-07
CHD1 and CHD2 subfamily	7	33.1×	4e-08
mRNA Splicing	6	28.6×	6e-07
mRNA Polyadenylation	7	26.7×	1e-07
Processing of Capped Intron-Containing Pre-mRNA	6	21.4×	2e-06
mRNA Splicing - Major Pathway	7	16.6×	1e-06
Metabolism of RNA	8	14.5×	6e-07

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	5	91.8×	8e-08
spliceosomal complex assembly	5	88.5×	8e-08
spliceosomal snRNP assembly	5	85.5×	8e-08
RNA splicing	9	23.4×	1e-08
mRNA splicing, via spliceosome	8	21.6×	8e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1690 predictions. Top by Δscore:

Variant	Effect	Δscore
22:29728624:CACCA:C	acceptor_loss	1.0000
22:29728626:CCA:C	acceptor_loss	1.0000
22:29728627:CAG:C	acceptor_loss	1.0000
22:29728628:A:C	acceptor_loss	1.0000
22:29728739:G:GT	donor_gain	1.0000
22:29728740:A:T	donor_gain	1.0000
22:29729049:C:A	acceptor_gain	1.0000
22:29729052:A:AG	acceptor_gain	1.0000
22:29729052:AAGT:A	acceptor_gain	1.0000
22:29729053:A:AG	acceptor_gain	1.0000
22:29729053:AGTGC:A	acceptor_gain	1.0000
22:29729054:G:GA	acceptor_gain	1.0000
22:29729054:GT:G	acceptor_gain	1.0000
22:29729054:GTGC:G	acceptor_gain	1.0000
22:29729054:GTGCG:G	acceptor_gain	1.0000
22:29729057:C:CA	acceptor_gain	1.0000
22:29729204:GGAGA:G	donor_gain	1.0000
22:29729205:GAGA:G	donor_gain	1.0000
22:29729205:GAGAG:G	donor_gain	1.0000
22:29729206:AGA:A	donor_gain	1.0000
22:29729207:GA:G	donor_gain	1.0000
22:29729207:GAG:G	donor_gain	1.0000
22:29729208:AGT:A	donor_loss	1.0000
22:29729209:G:GG	donor_gain	1.0000
22:29729209:GTGAG:G	donor_loss	1.0000
22:29729210:TGAGT:T	donor_loss	1.0000
22:29729211:GAGTG:G	donor_loss	1.0000
22:29729409:T:A	acceptor_gain	1.0000
22:29729417:C:A	acceptor_gain	1.0000
22:29729418:G:A	acceptor_gain	1.0000

AlphaMissense

1103 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:29748484:G:T	R21S	0.999
22:29740699:A:C	F74L	0.998
22:29740699:A:T	F74L	0.998
22:29740701:A:G	F74L	0.998
22:29740717:A:C	F68L	0.998
22:29740717:A:T	F68L	0.998
22:29740719:A:G	F68L	0.998
22:29740724:C:G	C66S	0.998
22:29740725:A:T	C66S	0.998
22:29742439:A:G	C57R	0.998
22:29748475:G:C	H24D	0.998
22:29748483:C:G	R21P	0.998
22:29748504:A:G	F14S	0.998
22:29748525:C:T	C7Y	0.998
22:29748526:A:G	C7R	0.998
22:29740706:C:G	C72S	0.997
22:29740707:A:G	C72R	0.997
22:29740707:A:T	C72S	0.997
22:29740725:A:G	C66R	0.997
22:29748465:C:T	G27E	0.997
22:29748473:G:C	H24Q	0.997
22:29748473:G:T	H24Q	0.997
22:29748503:G:C	F14L	0.997
22:29748503:G:T	F14L	0.997
22:29748505:A:G	F14L	0.997
22:29748516:C:A	C10F	0.997
22:29748516:C:G	C10S	0.997
22:29748516:C:T	C10Y	0.997
22:29748517:A:G	C10R	0.997
22:29748517:A:T	C10S	0.997

dbSNP variants (sampled 300 via entrez): RS1000000199 (22:29758454 AAC>A), RS1000288662 (22:29744189 G>C), RS1000314686 (22:29732869 T>A), RS1000363219 (22:29740021 T>TG,TGG), RS1000478546 (22:29738474 G>A,C), RS1000615055 (22:29738680 G>C), RS1000657441 (22:29734395 C>G), RS1000838142 (22:29750850 AG>A), RS1000840667 (22:29748241 G>C), RS1000889036 (22:29750428 A>T), RS1000937188 (22:29748806 G>A), RS1000959872 (22:29744302 A>C), RS1001128749 (22:29754734 C>G,T), RS1001264158 (22:29762692 C>T), RS1001318 (22:29736178 C>T)

Disease associations

OMIM: gene MIM:619741 | 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):

Study	Trait	p-value
GCST003974_1	Tonsillectomy	1.000000e-09
GCST004131_67	Inflammatory bowel disease	4.000000e-08
GCST004132_86	Crohn’s disease	8.000000e-07
GCST008058_139	Estimated glomerular filtration rate	5.000000e-15
GCST90002388_267	Lymphocyte count	1.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007924	tonsillectomy risk measurement
EFO:0004587	lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	increases expression, affects methylation	2
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
licochalcone B	increases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Disulfiram	affects binding, decreases expression	1
Doxorubicin	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methapyrilene	decreases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Thiram	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A8D8	SEES3-1V human ZMAT5, clone1	Embryonic stem cell	Male
CVCL_A8D9	SEES3-1V human ZMAT5, clone2	Embryonic stem cell	Male
CVCL_A8E0	SEES3-1V human ZMAT5, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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