MPHOSPH10

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

Basic information

Region (hg38): 2:71130309-71150101

Links

ENSG00000124383 ∙ NCBI:10199 ∙ OMIM:605503 ∙ HGNC:7213 ∙ Uniprot:O00566 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MPHOSPH10 gene.

• Inborn genetic diseases (23 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPHOSPH10 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20	4	4	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	3	4
Total	0	0	20	5	7

Variants in MPHOSPH10

This is a list of pathogenic ClinVar variants found in the MPHOSPH10 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-71130360-C-T			Likely benign (May 16, 2021)
2-71130375-C-T			Benign (Nov 16, 2018)
2-71130504-C-T			Benign (Jul 07, 2018)
2-71130580-G-C			Benign (Jul 07, 2018)
2-71130670-C-A		not specified	Uncertain significance (Nov 08, 2022)
2-71130751-T-A		not specified	Uncertain significance (Dec 22, 2023)
2-71132930-C-A			Benign (May 18, 2018)
2-71132953-T-C		not specified	Uncertain significance (Nov 07, 2022)
2-71132975-G-A		not specified	Likely benign (Oct 26, 2021)
2-71133151-C-T		not specified	Likely benign (Feb 11, 2022)
2-71133185-A-T		not specified	Uncertain significance (Feb 07, 2023)
2-71133226-G-A			Benign (Dec 31, 2019)
2-71133229-A-T		not specified	Likely benign (Dec 08, 2023)
2-71133236-A-G		not specified	Uncertain significance (Jul 14, 2022)
2-71133245-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-71133269-A-G			Benign (May 18, 2018)
2-71133364-G-A		not specified	Uncertain significance (Jan 04, 2024)
2-71133431-C-G		not specified	Uncertain significance (Sep 16, 2021)
2-71133481-G-C		not specified	Uncertain significance (Aug 26, 2022)
2-71133498-G-T		not specified	Uncertain significance (Aug 08, 2023)
2-71133509-T-A		not specified	Uncertain significance (Aug 30, 2022)
2-71133527-T-C			Benign (May 18, 2018)
2-71133952-G-A		not specified	Uncertain significance (Dec 16, 2022)
2-71134050-A-G		not specified	Likely benign (Jul 06, 2021)
2-71134081-C-T		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPHOSPH10	protein_coding	protein_coding	ENST00000244230	11	19788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.848	0.152	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.537	306	334	0.917	0.0000158	4565
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00116	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.0000373	0.0000352
Middle Eastern	0.00116	0.00114
South Asian	0.000171	0.000131
Other	0.00	0.00

dbNSFP

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.
• Pathway: 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 (Consensus)

Recessive Scores

• pRec: 0.0912

Intolerance Scores

• loftool: 0.651
• rvis_EVS: 1.87
• rvis_percentile_EVS: 97.2

Haploinsufficiency Scores

• pHI: 0.488
• hipred: Y
• hipred_score: 0.707
• ghis: 0.424

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mphosph10

Zebrafish Information Network

• Gene name: mphosph10
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: RNA splicing, via transesterification reactions;rRNA processing;RNA processing;RNA splicing;negative regulation of phosphatase activity
• Cellular component: nucleoplasm;chromosome;nucleolus;small nucleolar ribonucleoprotein complex;small-subunit processome;Mpp10 complex
• Molecular function: RNA binding;protein binding