MPHOSPH6

M-phase phosphoprotein 6

Basic information

Region (hg38): 16:82147797-82170224

Links

ENSG00000135698 ∙ NCBI:10200 ∙ OMIM:605500 ∙ HGNC:7214 ∙ Uniprot:Q99547 ∙ 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 MPHOSPH6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPHOSPH6 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				1	1	2
missense			12		1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	2

Variants in MPHOSPH6

This is a list of pathogenic ClinVar variants found in the MPHOSPH6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-82148763-C-T		not specified	Uncertain significance (Oct 12, 2022)
16-82148774-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-82148780-T-C		not specified	Uncertain significance (Feb 13, 2023)
16-82148792-T-G		not specified	Uncertain significance (Mar 29, 2024)
16-82148808-C-T		not specified	Uncertain significance (Nov 10, 2023)
16-82148813-T-C			Benign (Mar 29, 2018)
16-82148850-C-A		not specified	Uncertain significance (Jan 02, 2024)
16-82149361-C-G		not specified	Uncertain significance (Aug 10, 2021)
16-82149364-C-T		not specified	Uncertain significance (Dec 06, 2021)
16-82149368-T-C			Benign (Mar 29, 2018)
16-82151429-C-T		not specified	Uncertain significance (Jan 26, 2022)
16-82151430-C-G		not specified	Uncertain significance (Feb 28, 2023)
16-82151483-G-A			Likely benign (May 01, 2022)
16-82164089-C-G		not specified	Uncertain significance (Jun 16, 2024)
16-82164112-T-C		not specified	Uncertain significance (Dec 28, 2023)
16-82164174-G-C		not specified	Uncertain significance (Nov 08, 2022)
16-82170139-G-C		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPHOSPH6	protein_coding	protein_coding	ENST00000258169	5	22429

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000411	0.657	125723	0	24	125747	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.28	108	76.4	1.41	0.00000324	1061
Missense in Polyphen		25	20.004	1.2498		313
Synonymous	-2.09	37	24.0	1.54	0.00000104	251
Loss of Function	0.735	6	8.28	0.725	3.46e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000103	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that associates with the RNA exosome complex. Involved in the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and play a role in recruiting the RNA exosome complex to pre-rRNA; this function may include C1D. {ECO:0000269|PubMed:17412707, ECO:0000269|PubMed:26166824}.
• Pathway: RNA degradation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.741
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.504
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.578

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mphosph6

Gene ontology

• Biological process: maturation of 5.8S rRNA;rRNA processing
• Cellular component: nuclear exosome (RNase complex);exosome (RNase complex);nucleus;nucleoplasm;nucleolus;cytoplasm
• Molecular function: RNA binding;protein binding