MPHOSPH10

protein-coding

M-phase phosphoprotein 10, the group of Protein phosphatase 1 regulatory subunits|MPP10 subcomplex

Gene summary

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. [provided by RefSeq, Dec 2010]

MANE transcript

NM_005791.3

Inheritance

—

ClinVar variants

U:91B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr2:71,130,310-71,150,101

External References & Databases

Ensembl (ENSG00000124383)

Transcript & Mutation Effects

hg38 • Region Span ~19.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MPHOSPH10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 95

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005791.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			88 clinvar	9 clinvar	4 clinvar	101
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	91	9	4	104

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005791.3	RefSeq	NP_005782.1	11	MANE Select
ENST00000244230.7	Ensembl	ENSP00000244230.2	11	MANE Select
ENST00000468427.2	Ensembl	ENSP00000511582.1	10	Standard
ENST00000468427.3	Ensembl	ENSP00000511582.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
mphosph10	Danio rerio	Structure: head Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

mphosph10

Danio rerio

Structure: head

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

RNA splicing, via transesterification reactions
rRNA processing
RNA processing
RNA splicing
negative regulation of phosphatase activity

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
chromosome
nucleolus
small nucleolar ribonucleoprotein complex
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000244230
Coding exons: 11
Length: 19788
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125748
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.537	306	334	0.917	0.0000158	4565
Missense (PolyPhen)		105	125.32	0.83786		1788
Synonymous	-0.0475	120	119	1.01	0.00000570	1135
Loss of Function	4.32	6	32.6	0.184	0.00000167	435

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0012	0.0011	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.00017	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the 60-80S U3 small nucleolar ribonucleoprotein (U3 snoRNP). Required for the early cleavages during pre-18S ribosomal RNA processing.;

Recessive Scores

pRec: 0.0912

Intolerance Scores

LoFtool: 0.651
RVIS EVS: 1.87
RVIS percentile EVS: 97.2

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High