ZMAT4

Summary

ZMAT4 (zinc finger matrin-type 4, HGNC:25844) is a protein-coding gene on chromosome 8p11.21, encoding Zinc finger matrin-type protein 4 (Q9H898).

Enables identical protein binding activity. Predicted to be located in nucleus.

Source: NCBI Gene 79698 — RefSeq curated summary.

At a glance

• GWAS associations: 20
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_024645

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25844
Approved symbol	ZMAT4
Name	zinc finger matrin-type 4
Location	8p11.21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13842
Ensembl gene	ENSG00000165061
Ensembl biotype	protein_coding
Entrez	79698

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000297737, ENST00000315769, ENST00000518242, ENST00000519406, ENST00000519806, ENST00000522623, ENST00000523188, ENST00000523542, ENST00000523823, ENST00000917688, ENST00000958182, ENST00000958183

RefSeq mRNA: 2 — MANE Select: NM_024645 NM_001135731, NM_024645

CCDS: CCDS34885, CCDS47848

Canonical transcript exons

ENST00000297737 — 7 exons

Exon	Start	End
ENSE00001254491	40674704	40674931
ENSE00001254506	40581165	40581261
ENSE00001254514	40697245	40697401
ENSE00001638988	40530590	40532238
ENSE00002130411	40897683	40897826
ENSE00003482523	40767641	40767730
ENSE00003606486	40825575	40825680

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 90.51.

FANTOM5 (CAGE): breadth broad, TPM avg 3.5103 / max 285.8104, expressed in 399 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
92802	3.5103	399

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	90.51	gold quality
primary visual cortex	UBERON:0002436	85.64	gold quality
Brodmann (1909) area 23	UBERON:0013554	85.04	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.62	gold quality
Brodmann (1909) area 46	UBERON:0006483	83.42	gold quality
prefrontal cortex	UBERON:0000451	83.26	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.06	gold quality
lateral nuclear group of thalamus	UBERON:0002736	81.65	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.52	gold quality
right frontal lobe	UBERON:0002810	81.20	gold quality
frontal cortex	UBERON:0001870	81.19	gold quality
occipital lobe	UBERON:0002021	80.51	gold quality
neocortex	UBERON:0001950	80.27	gold quality
caudate nucleus	UBERON:0001873	79.91	gold quality
putamen	UBERON:0001874	79.72	gold quality
anterior cingulate cortex	UBERON:0009835	79.23	gold quality
cingulate cortex	UBERON:0003027	79.19	gold quality
calcaneal tendon	UBERON:0003701	79.14	gold quality
orbitofrontal cortex	UBERON:0004167	78.77	gold quality
superior frontal gyrus	UBERON:0002661	78.30	gold quality
pons	UBERON:0000988	78.28	gold quality
thyroid gland	UBERON:0002046	78.18	gold quality
nucleus accumbens	UBERON:0001882	77.92	gold quality
cerebral cortex	UBERON:0000956	77.89	gold quality
postcentral gyrus	UBERON:0002581	77.75	gold quality
left lobe of thyroid gland	UBERON:0001120	77.31	gold quality
telencephalon	UBERON:0001893	76.98	gold quality
right lobe of thyroid gland	UBERON:0001119	76.27	gold quality
parietal lobe	UBERON:0001872	75.75	gold quality
forebrain	UBERON:0001890	74.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	63.19
E-HCAD-25	yes	42.21
E-ANND-3	yes	4.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

93 targeting ZMAT4, 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-5193	100.00	67.26	1744
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-6817-3P	99.79	68.35	2126

Literature-anchored findings (GeneRIF, showing 2)

• Examines the expression of ZMAT4 mRNA in the samples with 1 or 2 copies of DNA, and observed a weak yet positive correlation between the relative expression level and gene dosage. (PMID:21269563)
• Association of VIPR2 and ZMAT4 with high myopia. (PMID:32166996)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	zmat4b	ENSDARG00000061419
danio_rerio	zmat4a	ENSDARG00000092987
mus_musculus	Zmat4	ENSMUSG00000037492
rattus_norvegicus	Zmat4	ENSRNOG00000042690
drosophila_melanogaster	CG1231	FBGN0035134
drosophila_melanogaster	dbf	FBGN0287630

Paralogs (9): ZNF346 (ENSG00000113761), ZNF385B (ENSG00000144331), ZMAT2 (ENSG00000146007), ZNF385D (ENSG00000151789), ZNF385A (ENSG00000161642), ZMAT1 (ENSG00000166432), KRCC1 (ENSG00000172086), ZMAT3 (ENSG00000172667), ZNF385C (ENSG00000187595)

Protein

Protein identifiers

Zinc finger matrin-type protein 4 — Q9H898 (reviewed: Q9H898)

All UniProt accessions (4): E5RFW2, E5RGZ7, E5RIF5, Q9H898

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H898-1	1	yes
Q9H898-2	2

RefSeq proteins (2): NP_001129203, NP_078921* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003604	Matrin/U1-like-C_Znf_C2H2	Domain
IPR013087	Znf_C2H2_type	Domain
IPR022755	Znf_C2H2_jaz	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR051868	ZN346_ZMAT4	Family

Pfam: PF12171, PF12874

UniProt features (8 total): zinc finger region 4, chain 1, region of interest 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H898-F1	74.09	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (6): DNA binding (GO:0003677), zinc ion binding (GO:0008270), identical protein binding (GO:0042802), nucleic acid binding (GO:0003676), 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:

Category	Terms
binding	2
nucleic acid binding	1
transition metal ion binding	1
protein binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

924 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMAT4	GJD2	Q9UKL4	567
ZMAT4	USHBP1	Q8N6Y0	535
ZMAT4	ITPRID1	Q6ZRS4	509
ZMAT4	FAM110A	Q9BQ89	489
ZMAT4	TM2D2	Q9BX73	489
ZMAT4	PRSS56	P0CW18	476
ZMAT4	BRF2	Q9HAW0	463
ZMAT4	DENND5B	Q6ZUT9	456
ZMAT4	SHISA6	Q6ZSJ9	445
ZMAT4	PLEKHA2	Q9HB19	439
ZMAT4	AGMO	Q6ZNB7	410
ZMAT4	LENG9	Q96B70	409
ZMAT4	CTXN1	P60606	408
ZMAT4	ITFG1	Q8TB96	400
ZMAT4	EFCAB5	A4FU69	389

IntAct

13 interactions, top by confidence:

A	B	Type	Score
CUL3	ZMAT4	psi-mi:“MI:0915”(physical association)	0.560
ZMAT4	CUL3	psi-mi:“MI:0915”(physical association)	0.560
ZMAT4	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
ZMAT4	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
M	ZMAT4	psi-mi:“MI:0915”(physical association)	0.370
PB1	ZMAT4	psi-mi:“MI:0915”(physical association)	0.370
NS	ZMAT4	psi-mi:“MI:0915”(physical association)	0.370
ZMAT4	VSIG8	psi-mi:“MI:0914”(association)	0.350
ZMAT4	PRKRA	psi-mi:“MI:0914”(association)	0.350
ZMAT4	RNF123	psi-mi:“MI:0914”(association)	0.350

BioGRID (41): ZMAT4 (Two-hybrid), ZMAT4 (Two-hybrid), FAM26D (Affinity Capture-MS), DSG4 (Affinity Capture-MS), HEPHL1 (Affinity Capture-MS), LYG2 (Affinity Capture-MS), S100A3 (Affinity Capture-MS), VSIG8 (Affinity Capture-MS), NEU2 (Affinity Capture-MS), TRIM29 (Affinity Capture-MS), LRRC15 (Affinity Capture-MS), ZMAT4 (Two-hybrid), ZMAT4 (Two-hybrid), ZMAT4 (Two-hybrid), ZMAT4 (Reconstituted Complex)

ESM2 similar proteins: A2RV29, A4QP16, B0JZ85, F4I7L1, O23463, O48772, O64571, P43243, P43244, Q0VD35, Q10KL8, Q28EG9, Q32NW2, Q3KQ71, Q569K4, Q5R4W8, Q5ZDJ6, Q66IH2, Q6AXX3, Q6NPP4, Q6PBT9, Q7XHR2, Q8BXJ8, Q8GSA7, Q8K310, Q8LMR2, Q8S9H7, Q90Y35, Q94AD9, Q9C682, Q9D8C3, Q9ERV1, Q9FFH1, Q9FH37, Q9FYG2, Q9H000, Q9H6B1, Q9H898, Q9LES2, Q9LES3

Diamond homologs: A2RV29, B0JZ85, O08781, O54836, Q0IIC4, Q0VD35, Q28EG9, Q5H9K5, Q5R4W8, Q8AVN9, Q8BZ94, Q9H898, Q9HA38, Q9R0B7, Q9UL40, O88532, Q08E27, Q12906, Q562A2, Q5R6Y5, Q5REX3, Q5U231, Q5ZIL4, Q6DCD0, Q6DD04, Q6GL57, Q6GPM1, Q6NXA4, Q6PCR6, Q7TP98, Q91550, Q91WM1, Q96KR1, Q96SI9, Q9JIL3, Q9JKU6, Q9UPR6, Q9Z1X4, Q17QQ9, Q5PPL1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4609 predictions. Top by Δscore:

Variant	Effect	Δscore
8:40532239:C:CC	acceptor_gain	1.0000
8:40581163:A:AC	donor_gain	1.0000
8:40581164:C:CC	donor_gain	1.0000
8:40697397:CTTCC:C	acceptor_gain	1.0000
8:40697400:CC:C	acceptor_gain	1.0000
8:40697401:CC:C	acceptor_gain	1.0000
8:40697402:C:CC	acceptor_gain	1.0000
8:40697405:C:CT	acceptor_gain	1.0000
8:40825569:CCTTA:C	donor_loss	1.0000
8:40825570:CTTA:C	donor_loss	1.0000
8:40825571:TTAC:T	donor_loss	1.0000
8:40825572:TACCT:T	donor_loss	1.0000
8:40825574:C:CG	donor_loss	1.0000
8:40825676:TCAGG:T	acceptor_gain	1.0000
8:40825677:CAGG:C	acceptor_gain	1.0000
8:40825677:CAGGC:C	acceptor_gain	1.0000
8:40825678:AGG:A	acceptor_gain	1.0000
8:40825679:GG:G	acceptor_gain	1.0000
8:40825680:GCTA:G	acceptor_loss	1.0000
8:40825681:C:CC	acceptor_gain	1.0000
8:40825681:CTAC:C	acceptor_loss	1.0000
8:40886360:T:TA	donor_gain	1.0000
8:40893166:AT:A	donor_gain	1.0000
8:40893167:T:TA	donor_gain	1.0000
8:40532235:CAGG:C	acceptor_gain	0.9900
8:40533280:TGA:T	donor_gain	0.9900
8:40533298:ATAAG:A	donor_gain	0.9900
8:40533299:T:C	donor_gain	0.9900
8:40539302:TGGC:T	donor_gain	0.9900
8:40697239:ACGT:A	donor_loss	0.9900

AlphaMissense

1495 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:40581183:C:T	G219E	1.000
8:40581184:C:G	G219R	1.000
8:40581184:C:T	G219R	1.000
8:40581191:A:C	H216Q	1.000
8:40581191:A:T	H216Q	1.000
8:40581193:G:C	H216D	1.000
8:40581193:G:T	H216N	1.000
8:40581196:C:G	A215P	1.000
8:40581202:A:C	Y213D	1.000
8:40581204:T:G	Q212P	1.000
8:40581214:A:G	S209P	1.000
8:40581230:G:C	C203W	1.000
8:40581231:C:A	C203F	1.000
8:40581231:C:G	C203S	1.000
8:40581231:C:T	C203Y	1.000
8:40581232:A:G	C203R	1.000
8:40581232:A:T	C203S	1.000
8:40581239:A:C	C200W	1.000
8:40581240:C:G	C200S	1.000
8:40581241:A:G	C200R	1.000
8:40581241:A:T	C200S	1.000
8:40674784:C:A	G166V	1.000
8:40674784:C:T	G166D	1.000
8:40674785:C:G	G166R	1.000
8:40674792:A:C	H163Q	1.000
8:40674792:A:T	H163Q	1.000
8:40674794:G:C	H163D	1.000
8:40674794:G:T	H163N	1.000
8:40674802:G:T	A160D	1.000
8:40674819:A:C	F154L	1.000

dbSNP variants (sampled 300 via entrez): RS1000001268 (8:40541481 T>A), RS1000004792 (8:40690470 C>G), RS1000014750 (8:40711574 T>C), RS1000017310 (8:40869048 C>G), RS1000021379 (8:40830385 C>T), RS1000023186 (8:40566349 A>C), RS1000026421 (8:40713641 G>A), RS1000037875 (8:40831412 C>G), RS1000039049 (8:40854998 G>A), RS1000046960 (8:40868800 C>T), RS1000061816 (8:40542348 T>C,G), RS1000079781 (8:40771768 G>A), RS1000084135 (8:40560764 A>G), RS1000089495 (8:40665967 C>T), RS1000111263 (8:40571332 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

20 associations (top):

Study	Trait	p-value
GCST000085_2	Fasting plasma glucose	9.000000e-06
GCST000085_3	Fasting plasma glucose	2.000000e-08
GCST001858_12	Refractive error	4.000000e-10
GCST002955_3	Forced expiratory volume in 1 second (occupational environmental exposures interaction)	7.000000e-08
GCST003455_21	Spherical equivalent (joint analysis main effects and education interaction)	4.000000e-09
GCST003455_44	Spherical equivalent (joint analysis main effects and education interaction)	1.000000e-07
GCST003997_23	Myopia	4.000000e-31
GCST004748_133	Lung cancer	7.000000e-06
GCST004797_4	Brain volume in infants (grey matter)	3.000000e-07
GCST006130_1	Pediatric areal bone mineral density (concordant skeletal phenotype)	3.000000e-08
GCST006130_2	Pediatric areal bone mineral density (concordant skeletal phenotype)	3.000000e-08
GCST006291_136	Spherical equivalent or myopia (age of diagnosis)	1.000000e-27
GCST007743_18	Iris color (L* coordinate)	7.000000e-06
GCST008151_76	Waist circumference	4.000000e-08
GCST008157_52	Body fat mass	2.000000e-06
GCST008160_114	Waist circumference	4.000000e-08
GCST008162_7	Hip circumference	2.000000e-06
GCST008526_70	Coffee consumption	4.000000e-06
GCST009734_4	Severe aplastic anemia	3.000000e-07
GCST010002_273	Refractive error	2.000000e-81

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004314	forced expiratory volume
EFO:0006993	response to mineral dust exposure
EFO:0004784	self reported educational attainment
EFO:0008368	infant grey matter volume measurement
EFO:0004847	age at onset
EFO:0009764	eye colour measurement
EFO:0006781	coffee consumption measurement
EFO:0006927	severe aplastic anemia

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs1367094	Efficacy	3	atenolol	Hypertension

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1367094	ZMAT4	3	0.00	1	atenolol

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	6
Benzo(a)pyrene	affects methylation, increases methylation	2
bisphenol A	increases methylation	1
benzo(e)pyrene	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Allergens	increases expression	1
Amphotericin B	increases expression	1
Atrazine	increases expression	1
Cisplatin	decreases expression	1
Copper	affects cotreatment, decreases expression	1
Dexamethasone	decreases expression	1
Methapyrilene	increases methylation	1
Oxygen	increases expression	1
Silicon Dioxide	decreases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
Okadaic Acid	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_A8D5	SEES3-1V human ZMAT4, clone1	Embryonic stem cell	Male
CVCL_A8D6	SEES3-1V human ZMAT4, clone2	Embryonic stem cell	Male
CVCL_A8D7	SEES3-1V human ZMAT4, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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