ZMAT1

Summary

ZMAT1 (zinc finger matrin-type 1, HGNC:29377) is a protein-coding gene on chromosome Xq22.1, encoding Zinc finger matrin-type protein 1 (Q5H9K5).

This gene encodes a protein containing Cys2-His2 (C2H2)-type zinc fingers, which are similar to those found in the nuclear matrix protein matrin 3. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 84460 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 112 total
• MANE Select transcript: NM_001394560

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29377
Approved symbol	ZMAT1
Name	zinc finger matrin-type 1
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1789
Ensembl gene	ENSG00000166432
Ensembl biotype	protein_coding
OMIM	301007
Entrez	84460

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000372782, ENST00000458570, ENST00000488347, ENST00000490757, ENST00000494068, ENST00000540921, ENST00000651725, ENST00000878189, ENST00000878190, ENST00000966029

RefSeq mRNA: 4 — MANE Select: NM_001394560 NM_001011657, NM_001282400, NM_001282401, NM_001394560

CCDS: CCDS35348, CCDS94643

Canonical transcript exons

ENST00000651725 — 6 exons

Exon	Start	End
ENSE00001458637	101882290	101884821
ENSE00003503232	101897868	101898042
ENSE00003510523	101904224	101904330
ENSE00003554317	101886632	101886731
ENSE00003635776	101898119	101898220
ENSE00003845432	101931717	101932027

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 96.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2139 / max 339.1804, expressed in 1139 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199964	7.6041	1116
199965	0.6098	312

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	96.10	gold quality
adenohypophysis	UBERON:0002196	95.67	gold quality
pituitary gland	UBERON:0000007	95.29	gold quality
sural nerve	UBERON:0015488	95.25	gold quality
left lobe of thyroid gland	UBERON:0001120	94.23	gold quality
thyroid gland	UBERON:0002046	93.97	gold quality
oviduct epithelium	UBERON:0004804	93.94	gold quality
right lobe of thyroid gland	UBERON:0001119	93.79	gold quality
tibial nerve	UBERON:0001323	93.77	gold quality
ventricular zone	UBERON:0003053	91.74	gold quality
epithelial cell of pancreas	CL:0000083	91.25	gold quality
corpus epididymis	UBERON:0004359	91.14	gold quality
left ovary	UBERON:0002119	90.82	gold quality
calcaneal tendon	UBERON:0003701	90.61	gold quality
corpus callosum	UBERON:0002336	89.43	gold quality
right ovary	UBERON:0002118	89.08	gold quality
right coronary artery	UBERON:0001625	89.02	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	88.92	gold quality
thymus	UBERON:0002370	88.90	gold quality
ovary	UBERON:0000992	88.71	gold quality
metanephros cortex	UBERON:0010533	88.70	gold quality
body of pancreas	UBERON:0001150	88.66	gold quality
spinal cord	UBERON:0002240	88.61	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.94	silver quality
nucleus accumbens	UBERON:0001882	87.68	gold quality
amygdala	UBERON:0001876	87.65	gold quality
popliteal artery	UBERON:0002250	87.52	gold quality
tibial artery	UBERON:0007610	87.52	gold quality
caudate nucleus	UBERON:0001873	87.46	gold quality
mucosa of stomach	UBERON:0001199	87.24	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.70
E-CURD-135	no	912.66
E-MTAB-4850	no	2.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

94 targeting ZMAT1, 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-1252-5P	100.00	69.80	2774
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-6809-3P	99.91	71.45	3814

Literature-anchored findings (GeneRIF, showing 2)

• Suggest that ZMAT1 transcript variant 2 is a potential diagnostic factor in patients with gastric cancer. (PMID:26191264)
• ZMAT1 acts as a tumor suppressor in pancreatic ductal adenocarcinoma by inducing SIRT3/p53 signaling pathway. (PMID:35392973)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zmat1	ENSDARG00000058679
mus_musculus	Zmat1	ENSMUSG00000052676
rattus_norvegicus	Zmat1	ENSRNOG00000024135
drosophila_melanogaster	CG1231	FBGN0035134
drosophila_melanogaster	dbf	FBGN0287630

Paralogs (9): ZNF346 (ENSG00000113761), ZNF385B (ENSG00000144331), ZMAT2 (ENSG00000146007), ZNF385D (ENSG00000151789), ZNF385A (ENSG00000161642), ZMAT4 (ENSG00000165061), KRCC1 (ENSG00000172086), ZMAT3 (ENSG00000172667), ZNF385C (ENSG00000187595)

Protein

Protein identifiers

Zinc finger matrin-type protein 1 — Q5H9K5 (reviewed: Q5H9K5)

All UniProt accessions (1): Q5H9K5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5H9K5-1	1	yes
Q5H9K5-2	2
Q5H9K5-3	3

RefSeq proteins (4): NP_001011657, NP_001269329, NP_001269330, NP_001381489* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003604	Matrin/U1-like-C_Znf_C2H2	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF12874

UniProt features (13 total): compositionally biased region 5, zinc finger region 3, splice variant 2, chain 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H9K5-F1	51.41	0.03

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): GCAAGGA_MIR502, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, WANG_TUMOR_INVASIVENESS_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, chrXq22, TTTGCAG_MIR518A2, LINDGREN_BLADDER_CANCER_CLUSTER_1_UP, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, PEDRIOLI_MIR31_TARGETS_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE14415_ACT_VS_CTRL_NATURAL_TREG_UP, GSE13547_2H_VS_12_H_ANTI_IGM_STIM_ZFX_KO_BCELL_UP, HES2_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), metal ion binding (GO:0046872)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMAT1	C3orf22	Q8N5N4	432
ZMAT1	DUXB	A0A1W2PPF3	423
ZMAT1	RNASE12	Q5GAN4	413
ZMAT1	TPRX1	Q8N7U7	408
ZMAT1	LCN6	P62502	394
ZMAT1	LEUTX	A8MZ59	387
ZMAT1	DUXA	A6NLW8	383
ZMAT1	SMIM17	P0DL12	380
ZMAT1	DRGX	A6NNA5	379
ZMAT1	C12orf56	Q8IXR9	378
ZMAT1	NEMP2	A6NFY4	373
ZMAT1	PABIR3	Q6P4D5	371
ZMAT1	ZNF836	Q6ZNA1	367
ZMAT1	UNCX	A6NJT0	366
ZMAT1	ALX3	O95076	366

IntAct

11 interactions, top by confidence:

A	B	Type	Score
ZMAT1	GORASP2	psi-mi:“MI:0915”(physical association)	0.550
ZMAT1	tax	psi-mi:“MI:0915”(physical association)	0.490
ZMAT1	H2AX	psi-mi:“MI:0915”(physical association)	0.400
ZMAT1	GRB2	psi-mi:“MI:0915”(physical association)	0.370
PIK3R3	ZMAT1	psi-mi:“MI:0915”(physical association)	0.370
FMR1	ZMAT1	psi-mi:“MI:0915”(physical association)	0.000
cls2	ZMAT1	psi-mi:“MI:0915”(physical association)	0.000
ZMAT1	fadL	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (33): ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Synthetic Lethality), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Affinity Capture-RNA), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid), ZMAT1 (Two-hybrid)

ESM2 similar proteins: A0JM80, A6H8Y1, A7MBJ2, D3ZF42, E9Q6J5, F4I700, F4J3S1, F4KCE9, F6QRE9, O04251, O82345, P23497, P46100, P48785, P48786, Q04996, Q05B65, Q0WTB8, Q13342, Q15361, Q32MZ4, Q3UZ39, Q3ZBR9, Q4QSC8, Q571C7, Q5H9K5, Q5RHP9, Q61687, Q66HF9, Q7YQM3, Q7YQM4, Q7Z5L2, Q8BJM3, Q8C4A5, Q8C9B9, Q8GZ87, Q8H991, Q8IW19, Q92576, Q940Y3

Diamond homologs: A0A096LPI5, A6NIU2, A6NJG6, F2Z398, P0DTE4, P51957, Q09FC8, Q5H9K5, Q5T7P6, Q68CZ1, Q6B4Z3, Q6UX73, Q86U02, Q8IV13, Q8N7M2, Q8N9N2, Q8NDZ0, Q8NEM8, Q8TDM0, Q92918, Q96J02, Q96MD7, Q9BUA6, Q9NXG0, A2RV29, B0JZ85, O08781, O54836, Q0IIC4, Q0VD35, Q28EG9, Q5R4W8, Q8AVN9, Q8BZ94, Q9H898, Q9HA38, Q9R0B7, Q9UL40, Q8N2A0, Q96M98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

926 predictions. Top by Δscore:

Variant	Effect	Δscore
X:101884817:ATTCT:A	acceptor_gain	1.0000
X:101884818:TTCT:T	acceptor_gain	1.0000
X:101884820:CT:C	acceptor_gain	1.0000
X:101884821:TC:T	acceptor_loss	1.0000
X:101884822:C:CC	acceptor_gain	1.0000
X:101884824:G:C	acceptor_gain	1.0000
X:101897862:CCTTA:C	donor_loss	1.0000
X:101897863:CTTAC:C	donor_loss	1.0000
X:101897864:TTA:T	donor_loss	1.0000
X:101897866:AC:A	donor_gain	1.0000
X:101897867:CC:C	donor_gain	1.0000
X:101897867:CCCAT:C	donor_gain	1.0000
X:101904219:CCTA:C	donor_loss	1.0000
X:101904220:CTAC:C	donor_loss	1.0000
X:101904221:TACC:T	donor_loss	1.0000
X:101904222:ACCTC:A	donor_loss	1.0000
X:101904223:C:CT	donor_loss	1.0000
X:101904288:T:C	donor_gain	1.0000
X:101904328:CGT:C	acceptor_gain	1.0000
X:101904329:GTCT:G	acceptor_loss	1.0000
X:101904330:TCTG:T	acceptor_loss	1.0000
X:101904331:C:CC	acceptor_gain	1.0000
X:101904331:CT:C	acceptor_loss	1.0000
X:101904332:T:C	acceptor_loss	1.0000
X:101904337:A:AC	acceptor_gain	1.0000
X:101884819:TCT:T	acceptor_gain	0.9900
X:101884820:CTC:C	acceptor_gain	0.9900
X:101884821:TCT:T	acceptor_gain	0.9900
X:101884822:C:A	acceptor_gain	0.9900
X:101884824:G:GC	acceptor_gain	0.9900

AlphaMissense

4633 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:101883534:C:A	W631C	0.996
X:101883534:C:G	W631C	0.996
X:101883536:A:G	W631R	0.994
X:101883536:A:T	W631R	0.994
X:101886658:G:C	H193Q	0.990
X:101886658:G:T	H193Q	0.990
X:101886660:G:C	H193D	0.989
X:101883527:A:G	S634P	0.988
X:101886640:A:C	H199Q	0.988
X:101886640:A:T	H199Q	0.988
X:101886668:A:G	F190S	0.987
X:101886708:A:G	C177R	0.987
X:101883535:C:G	W631S	0.985
X:101883513:A:C	F638L	0.984
X:101883513:A:T	F638L	0.984
X:101883515:A:G	F638L	0.984
X:101886685:A:C	F184L	0.983
X:101886685:A:T	F184L	0.983
X:101886686:A:G	F184S	0.983
X:101886687:A:G	F184L	0.983
X:101886697:A:C	C180W	0.983
X:101886699:A:G	C180R	0.982
X:101886706:G:C	C177W	0.982
X:101886642:G:C	H199D	0.981
X:101897983:A:C	F130L	0.981
X:101897983:A:T	F130L	0.981
X:101897985:A:G	F130L	0.981
X:101883538:A:G	L630P	0.980
X:101897956:G:C	H139Q	0.980
X:101897956:G:T	H139Q	0.980

dbSNP variants (sampled 300 via entrez): RS1000195964 (X:101909663 G>A,T), RS1000211268 (X:101918587 G>A), RS1000233292 (X:101924407 C>G,T), RS1000351001 (X:101902556 T>G), RS1000363227 (X:101913886 T>A,C), RS1000373813 (X:101927716 T>C,G), RS1000413696 (X:101907864 C>T), RS1000514343 (X:101922559 A>C,G), RS1000523236 (X:101933685 T>G), RS1000576157 (X:101911607 C>T), RS1000583142 (X:101922109 G>T), RS1000661855 (X:101925308 G>C), RS1000776974 (X:101933746 T>C), RS1000985360 (X:101889382 T>G), RS1001165761 (X:101892003 C>A)

Disease associations

OMIM: gene MIM:301007 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

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.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, decreases methylation, affects cotreatment	6
perfluorooctane sulfonic acid	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
perfluorooctanoic acid	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
perfluorohexanesulfonic acid	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Oxygen	increases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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