MPHOSPH10

Summary

MPHOSPH10 (M-phase phosphoprotein 10, HGNC:7213) is a protein-coding gene on chromosome 2p13.3, encoding U3 small nucleolar ribonucleoprotein protein MPP10 (O00566). Component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP). It is a common-essential gene (DepMap: required in 96.3% of cancer cell lines).

This gene encodes a protein that is phosphorylated during mitosis. The protein localizes to the nucleolus during interphase and to the chromosomes during M phase. The protein associates with the U3 small nucleolar ribonucleoprotein 60-80S complexes and may be involved in pre-rRNA processing.

Source: NCBI Gene 10199 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 115 total
• Cancer dependency (DepMap): dependent in 96.3% of screened cell lines (common-essential)
• MANE Select transcript: NM_005791

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7213
Approved symbol	MPHOSPH10
Name	M-phase phosphoprotein 10
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MPP10, MPP10P, CT90, PPP1R106
Ensembl gene	ENSG00000124383
Ensembl biotype	protein_coding
OMIM	605503
Entrez	10199

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay

ENST00000244230, ENST00000468427, ENST00000476969, ENST00000493360, ENST00000498451, ENST00000694907, ENST00000695484, ENST00000857231, ENST00000931987

RefSeq mRNA: 1 — MANE Select: NM_005791 NM_005791

CCDS: CCDS1916

Canonical transcript exons

ENST00000244230 — 11 exons

Exon	Start	End
ENSE00000846576	71138490	71138631
ENSE00000846577	71139795	71139862
ENSE00000846578	71141232	71141369
ENSE00000846579	71144428	71144538
ENSE00000846581	71149223	71149453
ENSE00003532216	71147999	71148106
ENSE00003694963	71133948	71134105
ENSE00003697000	71134626	71134797
ENSE00003699874	71132898	71133576
ENSE00003963953	71149866	71150101
ENSE00003963958	71130634	71130754

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 96.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.4122 / max 886.3918, expressed in 1809 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20881	34.1444	1802
20873	3.3631	1382
20880	0.6712	354
20879	0.6085	343
20874	0.4424	174
20878	0.1253	29
20875	0.0268	7
20876	0.0168	8
20877	0.0137	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	96.32	gold quality
tendon	UBERON:0000043	95.30	gold quality
tongue squamous epithelium	UBERON:0006919	94.51	gold quality
tendon of biceps brachii	UBERON:0008188	93.77	gold quality
cervix squamous epithelium	UBERON:0006922	93.23	gold quality
endometrium	UBERON:0001295	93.19	gold quality
cortical plate	UBERON:0005343	93.11	gold quality
cervix epithelium	UBERON:0004801	92.47	gold quality
squamous epithelium	UBERON:0006914	92.06	gold quality
esophagus mucosa	UBERON:0002469	92.00	gold quality
oral cavity	UBERON:0000167	91.81	gold quality
substantia nigra pars compacta	UBERON:0001965	91.79	gold quality
esophagus squamous epithelium	UBERON:0006920	91.79	gold quality
gluteal muscle	UBERON:0002000	91.61	gold quality
pericardium	UBERON:0002407	91.61	gold quality
pharyngeal mucosa	UBERON:0000355	91.58	gold quality
hair follicle	UBERON:0002073	91.58	gold quality
gastrocnemius	UBERON:0001388	91.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.47	gold quality
body of tongue	UBERON:0011876	91.42	gold quality
diaphragm	UBERON:0001103	91.28	gold quality
ganglionic eminence	UBERON:0004023	91.19	gold quality
gingival epithelium	UBERON:0001949	91.17	gold quality
tongue	UBERON:0001723	91.14	gold quality
superior surface of tongue	UBERON:0007371	91.09	gold quality
uterus	UBERON:0000995	90.98	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	90.96	gold quality
muscle of leg	UBERON:0001383	90.87	gold quality
gingiva	UBERON:0001828	90.85	gold quality
tibia	UBERON:0000979	90.84	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ENAD-17	no	284.87
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 96.3% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	mphosph10	ENSDARG00000012495
mus_musculus	Mphosph10	ENSMUSG00000030521
rattus_norvegicus	Mphosph10	ENSRNOG00000016266
drosophila_melanogaster	CG13097	FBGN0032051
caenorhabditis_elegans		WBGENE00013544

Protein

Protein identifiers

U3 small nucleolar ribonucleoprotein protein MPP10 — O00566 (reviewed: O00566)

Alternative names: M phase phosphoprotein 10

All UniProt accessions (5): A0A8Q3WK70, A0A8Q3WKB6, A0A8Q3WKH7, O00566, U3KQ48

UniProt curated annotations — full annotation on UniProt →

Function. Component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP). Required for the early cleavages during pre-18S ribosomal RNA processing. Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome.

Subunit / interactions. Part of the small subunit (SSU) processome, composed of more than 70 proteins and the RNA chaperone small nucleolar RNA (snoRNA) U3. Component of a heterotrimeric complex containing IMP3, IMP4 and MPHOSPH10. Interacts with IMP3 and IMP4.

Subcellular location. Nucleus. Nucleolus. Chromosome.

Post-translational modifications. Phosphorylated in M (mitotic) phase.

Similarity. Belongs to the MPP10 family.

RefSeq proteins (1): NP_005782* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR012173	Mpp10	Family

Pfam: PF04006

UniProt features (49 total): compositionally biased region 14, modified residue 10, coiled-coil region 7, sequence variant 7, cross-link 6, region of interest 4, chain 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7MQA	ELECTRON MICROSCOPY	2.7
7MQ8	ELECTRON MICROSCOPY	3.6
7MQ9	ELECTRON MICROSCOPY	3.87

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00566-F1	68.97	0.19

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 (16): 61, 120, 139, 163, 167, 171, 242, 275, 289, 609, 350, 382, 394, 555, 632, 649

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-6790901	rRNA modification in the nucleus and cytosol
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72312	rRNA processing
R-HSA-8868773	rRNA processing in the nucleus and cytosol
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 151 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_MATURATION_OF_SSU_RRNA, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_RNA_SPLICING, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, WESTON_VEGFA_TARGETS, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, WESTON_VEGFA_TARGETS_3HR, REACTOME_METABOLISM_OF_RNA

GO Biological Process (7): RNA splicing, via transesterification reactions (GO:0000375), RNA processing (GO:0006396), RNA splicing (GO:0008380), maturation of SSU-rRNA (GO:0030490), ribosomal small subunit biogenesis (GO:0042274), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (8): nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), sno(s)RNA-containing ribonucleoprotein complex (GO:0005732), small-subunit processome (GO:0032040), Mpp10 complex (GO:0034457), nucleus (GO:0005634), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	2
Metabolism of RNA	1
rRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
ribonucleoprotein complex biogenesis	2
ribosome biogenesis	2
nuclear lumen	2
intracellular membraneless organelle	2
nucleolus	2
nuclear protein-containing complex	2
RNA splicing	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
rRNA processing	1
ribosomal small subunit biogenesis	1
rRNA metabolic process	1
nucleic acid binding	1
binding	1
cellular anatomical structure	1
ribonucleoprotein complex	1
preribosome	1
t-UTP complex	1
90S preribosome	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

2109 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MPHOSPH10	FBL	P22087	834
MPHOSPH10	PWP2	Q15269	817
MPHOSPH10	RRP9	O43818	788
MPHOSPH10	HEATR1	Q9H583	736
MPHOSPH10	NOP58	Q9Y2X3	735
MPHOSPH10	COIL	P38432	734
MPHOSPH10	UTP25	Q68CQ4	729
MPHOSPH10	WDR43	Q15061	709
MPHOSPH10	WDR75	Q8IWA0	703
MPHOSPH10	UTP18	Q9Y5J1	673
MPHOSPH10	BMS1	Q14692	666
MPHOSPH10	NOP56	O00567	656
MPHOSPH10	UTP4	Q969X6	654
MPHOSPH10	UTP6	Q9NYH9	644
MPHOSPH10	CCNB1	P14635	638

IntAct

164 interactions, top by confidence:

A	B	Type	Score
IMP3	MPHOSPH10	psi-mi:“MI:0915”(physical association)	0.670
IMP3	MPHOSPH10	psi-mi:“MI:0914”(association)	0.670
rep	MPHOSPH10	psi-mi:“MI:0914”(association)	0.660
MPHOSPH10	rep	psi-mi:“MI:0915”(physical association)	0.660
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
PPP1CA	MPHOSPH10	psi-mi:“MI:0407”(direct interaction)	0.590
PPP1CA	MPHOSPH10	psi-mi:“MI:0915”(physical association)	0.590
MORF4L1	MPHOSPH10	psi-mi:“MI:0915”(physical association)	0.560
CTNNA3	MPHOSPH10	psi-mi:“MI:0915”(physical association)	0.560
BYSL	MPHOSPH10	psi-mi:“MI:0915”(physical association)	0.560
MPHOSPH10	MORF4L1	psi-mi:“MI:0915”(physical association)	0.560
MPHOSPH10	CTNNA3	psi-mi:“MI:0915”(physical association)	0.560
MPHOSPH10	BYSL	psi-mi:“MI:0915”(physical association)	0.560
IMP4	MPHOSPH10	psi-mi:“MI:0915”(physical association)	0.560
FGF3	GTPBP10	psi-mi:“MI:0914”(association)	0.530
H1-6	ZNF724	psi-mi:“MI:0914”(association)	0.530
RPS2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
ZNF2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530

BioGRID (229): MPHOSPH10 (Affinity Capture-MS), MPHOSPH10 (Affinity Capture-MS), MPHOSPH10 (Affinity Capture-MS), DDX52 (Co-fractionation), DDX56 (Co-fractionation), DKC1 (Co-fractionation), IMP3 (Co-fractionation), IMP4 (Co-fractionation), MPHOSPH10 (Co-fractionation), MPHOSPH10 (Co-fractionation), MPHOSPH10 (Co-fractionation), MPHOSPH10 (Co-fractionation), MPHOSPH10 (Co-fractionation), MPHOSPH10 (Co-fractionation), MPHOSPH10 (Co-fractionation)

ESM2 similar proteins: A0A286Y9D1, C0HKD8, C0HKD9, F4HVZ5, F4IDY7, F4IP06, O00566, O14012, O15541, O48713, O94416, O94667, O94880, P34648, P38326, P55080, P55081, Q05021, Q10580, Q14320, Q15906, Q16U25, Q17QX9, Q28BK4, Q2VPH1, Q4KLV7, Q568K9, Q5E9F6, Q5EA98, Q5R5V9, Q5XIB2, Q62481, Q67ER4, Q6FML0, Q6GNJ8, Q6NXY9, Q754T8, Q7KN79, Q7PYQ5, Q810V0

Diamond homologs: O00566, O13910, Q810V0, Q9FJY5, P47083

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
MPHOSPH10	“up-regulates activity”	IMP3	binding
MPHOSPH10	“up-regulates activity”	IMP4	binding
MPHOSPH10	“up-regulates activity”	RPS5	binding
MPHOSPH10	“up-regulates activity”	UTP3	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 134 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
Formation of Senescence-Associated Heterochromatin Foci (SAHF)	5	40.5×	9e-07
Peptide chain elongation	26	39.8×	8e-34
Viral mRNA Translation	26	39.8×	8e-34
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	26	39.3×	8e-34
Selenocysteine synthesis	26	37.7×	2e-33
Eukaryotic Translation Termination	26	37.7×	2e-33
Eukaryotic Translation Initiation	10	37.2×	1e-12
Cap-dependent Translation Initiation	10	37.2×	1e-12

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of DNA recombination	6	55.7×	6e-08
chromosome condensation	7	48.8×	7e-09
cytoplasmic translation	27	41.3×	2e-34
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	6	33.4×	2e-06
translation	26	22.1×	2e-25
ribosomal small subunit biogenesis	11	20.7×	7e-10
rRNA processing	16	18.7×	5e-14
ribosomal large subunit biogenesis	5	18.3×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	86
Likely benign	9
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1526 predictions. Top by Δscore:

Variant	Effect	Δscore
2:71130755:G:GG	donor_gain	1.0000
2:71133560:G:GT	donor_gain	1.0000
2:71133572:TTAAG:T	donor_loss	1.0000
2:71133573:TAAG:T	donor_loss	1.0000
2:71133574:AAGG:A	donor_loss	1.0000
2:71133576:GGTAA:G	donor_loss	1.0000
2:71133577:G:C	donor_loss	1.0000
2:71133578:T:G	donor_loss	1.0000
2:71133941:A:AG	acceptor_gain	1.0000
2:71133946:A:AG	acceptor_gain	1.0000
2:71133947:G:GT	acceptor_gain	1.0000
2:71133947:GT:G	acceptor_gain	1.0000
2:71133947:GTC:G	acceptor_gain	1.0000
2:71133947:GTCA:G	acceptor_gain	1.0000
2:71134086:GAAC:G	donor_gain	1.0000
2:71134089:C:CG	donor_gain	1.0000
2:71134089:C:G	donor_gain	1.0000
2:71134101:GAAAC:G	donor_gain	1.0000
2:71134102:AAAC:A	donor_gain	1.0000
2:71134103:AAC:A	donor_gain	1.0000
2:71134104:AC:A	donor_gain	1.0000
2:71134105:CG:C	donor_loss	1.0000
2:71134106:G:GG	donor_gain	1.0000
2:71134107:TGA:T	donor_loss	1.0000
2:71134108:G:GC	donor_loss	1.0000
2:71134109:AG:A	donor_loss	1.0000
2:71134608:A:G	acceptor_gain	1.0000
2:71134621:TGTA:T	acceptor_loss	1.0000
2:71134624:A:AG	acceptor_gain	1.0000
2:71134624:A:C	acceptor_loss	1.0000

AlphaMissense

4604 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:71138541:T:A	W384R	0.999
2:71138541:T:C	W384R	0.999
2:71138543:G:C	W384C	0.999
2:71138543:G:T	W384C	0.999
2:71138576:G:C	R395S	0.998
2:71138576:G:T	R395S	0.998
2:71138575:G:C	R395T	0.997
2:71139850:G:C	R432S	0.996
2:71139850:G:T	R432S	0.996
2:71138548:T:C	L386P	0.995
2:71138586:A:C	S399R	0.995
2:71138588:C:A	S399R	0.995
2:71138588:C:G	S399R	0.995
2:71138590:T:C	L400P	0.994
2:71139840:T:A	I429N	0.994
2:71139849:G:C	R432T	0.994
2:71141235:T:A	W438R	0.994
2:71141235:T:C	W438R	0.994
2:71139828:T:C	L425P	0.993
2:71144501:T:C	L507S	0.993
2:71144506:G:C	A509P	0.993
2:71139849:G:T	R432M	0.992
2:71141329:T:A	L469H	0.992
2:71149284:G:C	R576P	0.992
2:71138553:G:A	G388R	0.991
2:71138553:G:C	G388R	0.991
2:71138610:T:C	F407L	0.991
2:71138612:T:A	F407L	0.991
2:71138612:T:G	F407L	0.991
2:71141325:A:C	S468R	0.991

dbSNP variants (sampled 300 via entrez): RS1000154373 (2:71143448 AT>A), RS1000367572 (2:71137330 A>T), RS1000382450 (2:71136841 T>G), RS1000408593 (2:71150340 G>A), RS1000689696 (2:71134003 G>A,C), RS1001026628 (2:71148283 A>T), RS1001042254 (2:71146272 G>A), RS1001225737 (2:71142701 T>C), RS1001278186 (2:71142986 T>C), RS1001346356 (2:71145251 G>A), RS1001370580 (2:71144915 T>A), RS1001566341 (2:71138658 A>C,G,T), RS1002220685 (2:71136536 G>A,C), RS1002319437 (2:71141463 C>A), RS1002360926 (2:71132321 A>G)

Disease associations

OMIM: gene MIM:605503 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST005196_203	Coronary artery disease	3.000000e-06
GCST009391_1014	Metabolite levels	1.000000e-06
GCST009391_1221	Metabolite levels	5.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010360	lysophosphatidylcholine 18:1 measurement
EFO:0010421	triacylglycerol 54:3 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Arsenic	affects methylation, increases abundance, increases expression	2
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases abundance, increases expression	1
cobaltous chloride	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
K 7174	decreases expression	1
Acetaminophen	decreases expression	1
Atrazine	increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Doxorubicin	decreases expression	1
Ivermectin	decreases expression	1
Ribonucleotides	affects binding	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Vitamin E	decreases expression	1
Cyclosporine	increases expression	1
Sodium Selenite	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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