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 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11). Located in nucleoplasm. Part of U12-type spliceosomal complex.

Source: NCBI Gene 55954 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 24 total
• GTEx eGene: eQTL in 12 tissues, sQTL in 4 (q < 0.05)
• Cancer dependency (DepMap): dependent in 98.0% of screened cell lines (common-essential)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.33 (unconstrained)
• 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: 37 — 34 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

MANE Select: ENST00000344318

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1

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, ENST00000975289, ENST00000975290, ENST00000975291, ENST00000975292, ENST00001088960, ENST00001093623, ENST00001093624, ENST00001093625, ENST00001131597

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.

Highest expression (Bgee): hindlimb stylopod muscle, apex of heart, granulocyte, gastrocnemius, muscle of leg.

Genetic regulation across tissues (GTEx eQTL / sQTL)

ZMAT5 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 12 tissues and its splicing (sQTL) in 4 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

16 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	eqtl	3.5e-09	-0.31	22:29727021:G:A
Skin Not Sun Exposed Suprapubic	eqtl	5.9e-09	-0.37	22:29805392:C:T
Cells EBV-transformed lymphocytes	eqtl	8.2e-09	-0.45	22:29992769:T:G
Nerve Tibial	eqtl	2.8e-06	-0.48	22:29838480:T:C
Colon Sigmoid	sqtl	5.1e-04	+0.89	22:29224472:T:C
Artery Aorta	sqtl	6.2e-03	+1.24	22:30546714:G:A
Skin Sun Exposed Lower leg	sqtl	6.7e-03	+0.32	22:29425860:C:T
Stomach	eqtl	1.0e-02	-0.33	22:29765812:A:G
Esophagus Mucosa	eqtl	1.5e-02	-0.67	22:29220957:G:A
Cells Cultured fibroblasts	eqtl	2.0e-02	+0.41	22:30655822:C:T
Whole Blood	eqtl	2.6e-02	-0.06	22:29840254:G:T
Brain Frontal Cortex BA9	eqtl	2.6e-02	-0.35	22:30456799:T:C
Lung	eqtl	2.7e-02	-0.25	22:29468643:C:T
Testis	sqtl	3.6e-02	-1.43	22:29196239:C:T
Breast Mammary Tissue	eqtl	3.9e-02	+0.11	22:30437698:C:CG
Brain Caudate basal ganglia	eqtl	4.0e-02	-0.30	22:29502202:A:G

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

showing 100 of 266 tissues 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
lower esophagus mucosa	UBERON:0035834	85.31	gold quality
left coronary artery	UBERON:0001626	85.21	gold quality
heart left ventricle	UBERON:0002084	85.07	gold quality
right lobe of thyroid gland	UBERON:0001119	85.06	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.01	gold quality
prefrontal cortex	UBERON:0000451	84.93	gold quality
right coronary artery	UBERON:0001625	84.93	gold quality
right frontal lobe	UBERON:0002810	84.89	gold quality
esophagus	UBERON:0001043	84.75	gold quality
adrenal gland	UBERON:0002369	84.74	gold quality
aorta	UBERON:0000947	84.73	gold quality
ventricular zone	UBERON:0003053	84.72	gold quality
left lobe of thyroid gland	UBERON:0001120	84.61	gold quality
esophagus mucosa	UBERON:0002469	84.31	gold quality
amygdala	UBERON:0001876	84.29	gold quality
cardiac ventricle	UBERON:0002082	84.29	gold quality
muscle organ	UBERON:0001630	84.26	gold quality
mucosa of transverse colon	UBERON:0004991	84.25	gold quality
popliteal artery	UBERON:0002250	84.20	gold quality
tibial artery	UBERON:0007610	84.19	gold quality
body of pancreas	UBERON:0001150	84.16	gold quality
spinal cord	UBERON:0002240	84.14	gold quality
body of uterus	UBERON:0009853	84.10	gold quality
ectocervix	UBERON:0012249	84.09	gold quality
caudate nucleus	UBERON:0001873	83.81	gold quality
right ovary	UBERON:0002118	83.76	gold quality
metanephros cortex	UBERON:0010533	83.54	gold quality
coronary artery	UBERON:0001621	83.50	gold quality
cardiac atrium	UBERON:0002081	83.43	gold quality
skin of leg	UBERON:0001511	83.41	gold quality
left uterine tube	UBERON:0001303	83.23	gold quality
endocervix	UBERON:0000458	83.13	gold quality
mucosa of stomach	UBERON:0001199	83.09	gold quality
thyroid gland	UBERON:0002046	83.01	gold quality
heart	UBERON:0000948	83.00	gold quality
skin of abdomen	UBERON:0001416	82.99	gold quality
nucleus accumbens	UBERON:0001882	82.89	gold quality
minor salivary gland	UBERON:0001830	82.87	gold quality
islet of Langerhans	UBERON:0000006	82.70	gold quality
putamen	UBERON:0001874	82.67	gold quality
cortical plate	UBERON:0005343	82.63	gold quality
right lung	UBERON:0002167	82.56	gold quality
stomach	UBERON:0000945	82.42	gold quality
spleen	UBERON:0002106	82.40	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	82.27	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.25	gold quality
pancreas	UBERON:0001264	82.23	gold quality
left ovary	UBERON:0002119	82.13	gold quality
blood	UBERON:0000178	82.02	gold quality
transverse colon	UBERON:0001157	81.88	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.82	gold quality
omental fat pad	UBERON:0010414	81.64	gold quality
upper lobe of left lung	UBERON:0008952	81.60	gold quality
cerebellar hemisphere	UBERON:0002245	81.56	gold quality
peritoneum	UBERON:0002358	81.56	gold quality
cerebellar cortex	UBERON:0002129	81.44	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.24	gold quality
small intestine Peyer’s patch	UBERON:0003454	81.22	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.08	gold quality
gall bladder	UBERON:0002110	81.07	gold quality
neocortex	UBERON:0001950	80.58	gold quality
saliva-secreting gland	UBERON:0001044	80.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.08	gold quality
zone of skin	UBERON:0000014	79.88	gold quality
mouth mucosa	UBERON:0003729	79.81	gold quality
frontal cortex	UBERON:0001870	79.75	gold quality
subcutaneous adipose tissue	UBERON:0002190	79.38	gold quality
cerebellum	UBERON:0002037	79.37	gold quality
hypothalamus	UBERON:0001898	79.25	gold quality
small intestine	UBERON:0002108	79.07	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Frontal cortex	tissue	50.8
Hippocampal formation	tissue	49.3
Caudate putamen	tissue	43.7
Spinal cord	tissue	39.8
Skeletal muscle	tissue	34.7	medium
Medulla oblongata	tissue	26.0
Thalamus	tissue	25.8
Corpus callosum	tissue	24.1
Tongue	tissue	22.8
Pons	tissue	22.7
Parathyroid gland	tissue	21.6	medium
Midbrain	tissue	20.4
Superior colliculi	tissue	20.2
Fallopian tube	tissue	19.3	medium
Heart muscle	tissue	19.1	medium
Epididymis	tissue	18.7	medium
Salivary gland	tissue	17.2	medium
Putamen	tissue	17.0
Substantia nigra	tissue	17.0
Periaqueductal gray	tissue	16.9
Thymus	tissue	16.6
Ovary	tissue	16.1	low
Seminal vesicle	tissue	15.7	medium
Liver	tissue	15.7	high
Choroid plexus	tissue	15.3
Adrenal gland	tissue	14.5	medium
Vagina	tissue	14.3	medium
Pancreas	tissue	14.3	medium
Lymph node	tissue	14.1	high
Cerebral cortex	tissue	14.1	high
Locus coeruleus	tissue	14.1
Ventral forebrain	tissue	14.1
Somatosensory cortex	tissue	14.1
Hippocampus	tissue	13.7	medium
Cerebellum	tissue	13.6	medium
Septum	tissue	13.6
Hypothalamus	tissue	13.4
Thyroid gland	tissue	13.4	medium
Bone marrow	tissue	13.4	medium
Postcentral gyrus	tissue	13.3
Nucleus accumbens	tissue	13.0
Smooth muscle	tissue	12.9	medium
Lung	tissue	12.6	high
Prostate	tissue	11.9	medium
Spleen	tissue	11.8	high
Esophagus	tissue	11.7	high
Duodenum	tissue	11.5	high
Amygdala	tissue	11.4
Tonsil	tissue	11.4	high
Basal ganglia	tissue	11.1	high
Occipital cortex	tissue	11.1
Stomach 1	tissue	11.0	medium
Cervix	tissue	10.9	medium
Motor cortex	tissue	10.3
Retrosplenial cortex	tissue	10.2
Temporal cortex	tissue	10.2
Kidney	tissue	10.1	high
Olfactory bulb	tissue	10.0
Appendix	tissue	10.0	medium
Skin 1	tissue	9.9	medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Ventral hippocampus (49.3), Dorsal hippocampus (40.4), Ventral spinal cord (39.8), Dorsal spinal cord (25.0), White matter (24.1).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting ZMAT5 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

18 miRNAs:

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

gnomAD constraint: pLI 3.46e-08, LOEUF 1.33, missense Z 0.666 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000344318 — one region, missense o/e 0.81. DepMap (CRISPR cell-line fitness): dependent in 98.0% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): Calu-6 (-2.394), HCC38 (-2.209), OCI-My7 (-1.787), SK-N-AS (-1.737), HEL 92.1.7 (-1.606), SW837 (-1.589), OCUM-1 (-1.576), HEL (-1.551), RERF-GC-1B (-1.551), NCI-H1694 (-1.544), SK-N-BE(2) (-1.534), COR-L279 (-1.532), SK-N-FI (-1.523), CL-11 (-1.502), JM1 (-1.495).

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

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1914428) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 4 distinct phenotype terms.

Mouse phenotype (MP)	Records
increased circulating aspartate transaminase level	1
cornea deposits	1
increased grip strength	1
preweaning lethality, complete penetrance	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	Q2TA39	94.1%	Diamond
Oryza sativa Japonica Group	Q0JP11	76.2%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CABP7-DT	ncRNA	122149303
CABP7	protein-coding	164633
NF2	protein-coding	4771
NIPSNAP1	protein-coding	8508
THOC5	protein-coding	8563
UQCR10	protein-coding	29796
ASCC2	protein-coding	84164
MTMR3	protein-coding	8897

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 (13 total): helix 6, strand 3, chain 1, zinc finger region 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

5 structures by resolution:

PDB	Title	Method	Resolution (Å)
9GCL	Structure of the U11 snRNP C-lobe	ELECTRON MICROSCOPY	3
9GC0	3’-lobe of the substrate-bound U11 snRNP	ELECTRON MICROSCOPY	3.2
8Y6O	Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and …	ELECTRON MICROSCOPY	3.38
8R7N	Overall structure of the U11 snRNP	ELECTRON MICROSCOPY	3.4
9GBW	Overall structure of the substrate-bound U11 snRNP	ELECTRON MICROSCOPY	3.5

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH approved · IF supported

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

ID	Pathway	Evidence
R-HSA-72165	mRNA Splicing - Minor Pathway	curated
R-HSA-8953854	Metabolism of RNA	—
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA	—
R-HSA-72172	mRNA Splicing	—

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 (4): spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) (GO:0000388), mRNA splicing, via spliceosome (GO:0000398), RNA splicing (GO:0008380), mRNA processing (GO:0006397)

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

3 top-level categories:

Category	Pathways
mRNA Splicing	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1

GO top-level categories

15 GO namespaces:

Category	Terms
RNA processing	2
spliceosomal conformational changes to generate catalytic conformation	1
protein-RNA complex assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 11 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
U12-type spliceosomal complex	CC	direct assay
nucleoplasm	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 1,106 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMAT5	SNRNP35	Q16560	741
ZMAT5	SNRNP25	Q9BV90	661
ZMAT5	SNRNP48	Q6IEG0	638
ZMAT5	ASCC2	Q9H1I8	602
ZMAT5	ZCRB1	Q8TBF4	598
ZMAT5	CABP7	Q86V35	586
ZMAT5	RASL10A	Q92737	573
ZMAT5	RNPC3	Q96LT9	554
ZMAT5	GAS2L1	Q99501	552
ZMAT5	THOC5	Q13769	551
ZMAT5	CCDC157	Q569K6	534
ZMAT5	SPATA9	Q9BWV2	521
ZMAT5	SNRPF	P62306	512
ZMAT5	SYTL3	Q4VX76	509
ZMAT5	EMID1	Q96A84	498

IntAct

Human interaction partners of ZMAT5 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

20 partners by confidence:

Partner	Interaction type	MIscore	Records
AIRIM	physical association	0.560	3
ARMC7	physical association	0.560	3
BYSL	physical association	0.560	3
CCDC120	physical association	0.560	3
CREB5	physical association	0.560	3
FANCL	physical association	0.560	3
GEM	physical association	0.560	3
GPANK1	physical association	0.560	3
HOXC8	physical association	0.560	3
MLH1	physical association	0.560	3
PIH1D2	physical association	0.560	3
PLEKHA7	physical association	0.560	3
RBPMS2	physical association	0.560	3
SMARCD1	physical association	0.560	3
TCHP	physical association	0.560	3
TRIM41	physical association	0.560	3
VPS37C	physical association	0.560	3
ZNF417	physical association	0.560	3
DENND4B	association	0.530	2
DCAF10	association	0.350	1

BioGRID (80 interactions; top human partners by supporting records): ZRSR2 (Affinity Capture-MS; 3 records), ACTA2 (Affinity Capture-MS; 2 records), ACTBL2 (Affinity Capture-MS; 2 records), CTU2 (Affinity Capture-MS; 2 records), DENND4B (Affinity Capture-MS; 2 records), GSTT1 (Affinity Capture-MS; 2 records), PDCD7 (Affinity Capture-MS; 2 records), PSMG3 (Affinity Capture-MS; 2 records), PSMG4 (Affinity Capture-MS; 2 records), RNPC3 (Affinity Capture-MS; 2 records), SNRNP48 (Affinity Capture-MS; 2 records), SNRPE (Affinity Capture-MS; 2 records), SNRPF (Affinity Capture-MS; 2 records), SNRPG (Affinity Capture-MS; 2 records), SNRPN (Affinity Capture-MS; 2 records)

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

Complex	Subunits	Members
18S U11/U12 snRNP	24	PRPF8, RNPC3, SF3B2, SF3B4, SF3B5, SNRPD2, YBX1, SF3B1, SNRNP35, SNRNP48, SNRPE, ZCRB1, ZMAT5, ZRSR2, SNRPB, DHX15, PDCD7, SF3B3, SNRPD1, SNRPD3, SNRPF, SF3B6, SNRNP25, SNRPG

Disease & clinical

Genetic variants

Variant evidence for ZMAT5: 24 ClinVar records (0 pathogenic / likely pathogenic); 5 GWAS associations.

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

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 40 predictions of 622):

Position(s)	Effect	Δscore	Sites
22:29738328–29738329	donor_loss	1.0000	4
22:29742416–29742417	donor_loss	1.0000	3
22:29742481–29742482	acceptor_loss	1.0000	6
22:29748572–29748573	acceptor_loss	1.0000	6
22:29738328–29738329	donor_loss	0.9900	2
22:29738442	acceptor_gain	0.9900
22:29738442–29738443	acceptor_loss	0.9900	5
22:29740648–29740649	donor_loss	0.9900	5
22:29740731–29740732	acceptor_loss	0.9900	6
22:29742416–29742417	donor_loss	0.9900	2

AlphaMissense

365 missense substitutions predicted likely pathogenic (of 1,103 scored), across 82 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
H24	8	0.990	0.998
H30	8	0.984	0.996
F14	8	0.981	0.998
H76	8	0.974	0.993
D16	8	0.970	0.994
D8	8	0.874	0.952
C7	7	0.996	0.998
C10	7	0.995	0.997
C57	7	0.994	0.998
C72	7	0.994	0.997
C66	7	0.993	0.998
F68	7	0.987	0.998
F74	7	0.987	0.998
F60	7	0.944	0.985
W37	7	0.938	0.967
F41	7	0.915	0.984
W169	7	0.873	0.972
W113	7	0.864	0.937
E51	7	0.814	0.892
D43	7	0.796	0.916

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (validation)	unfavorable	0.000136
Head and Neck Squamous Cell Carcinoma (TCGA)	favorable	0.00056

Disease associations

OMIM: gene MIM:619741 | disease phenotypes:

GWAS associations

5 associations:

Study	Trait	p-value
GCST008058_139	Estimated glomerular filtration rate	5e-15
GCST90002388_367	Lymphocyte count	1e-11
GCST003974_1	Tonsillectomy	1e-9
GCST004131_67	Inflammatory bowel disease	4e-8
GCST004132_71	Crohn’s disease	8e-7

EFO canonical traits (from GWAS)

2 canonical traits:

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 (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	affects methylation, increases expression	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	decreases expression, affects binding	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)

Via MONDO — disease-level, not drug-specific.