MPHOSPH9

M-phase phosphoprotein 9

Basic information

Region (hg38): 12:123152319-123244014

Links

ENSG00000051825 ∙ NCBI:10198 ∙ OMIM:605501 ∙ HGNC:7215 ∙ Uniprot:Q99550 ∙ 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 MPHOSPH9 gene.

• Inborn genetic diseases (46 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPHOSPH9 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			42	4		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	4	0

Variants in MPHOSPH9

This is a list of pathogenic ClinVar variants found in the MPHOSPH9 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-123156827-G-A		not specified	Uncertain significance (Aug 19, 2023)
12-123156853-A-G		not specified	Uncertain significance (Jun 18, 2021)
12-123161321-C-T		not specified	Uncertain significance (May 09, 2022)
12-123161323-G-A		not specified	Likely benign (Jun 06, 2023)
12-123161332-C-A		not specified	Uncertain significance (Sep 16, 2021)
12-123161357-C-A		not specified	Uncertain significance (May 31, 2023)
12-123161357-C-T		not specified	Uncertain significance (Feb 06, 2024)
12-123162187-C-T		not specified	Uncertain significance (Apr 18, 2023)
12-123162193-C-G		not specified	Uncertain significance (Jun 11, 2021)
12-123163095-T-C		not specified	Uncertain significance (Sep 26, 2022)
12-123164015-C-T		not specified	Uncertain significance (Dec 02, 2021)
12-123164027-T-C		not specified	Uncertain significance (Aug 08, 2023)
12-123164040-T-C		not specified	Uncertain significance (May 24, 2023)
12-123164046-G-C		not specified	Uncertain significance (Mar 06, 2023)
12-123164051-C-T		not specified	Uncertain significance (Apr 05, 2023)
12-123165347-A-G		not specified	Uncertain significance (Dec 17, 2021)
12-123165355-C-T		not specified	Likely benign (Jul 07, 2022)
12-123166730-G-T		not specified	Uncertain significance (Apr 04, 2023)
12-123166733-T-C		not specified	Uncertain significance (Jul 21, 2021)
12-123166770-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-123176727-C-T		not specified	Uncertain significance (Jan 24, 2024)
12-123181203-C-T		not specified	Uncertain significance (Aug 02, 2022)
12-123194395-C-T		not specified	Uncertain significance (Jan 26, 2023)
12-123194418-G-C		not specified	Likely benign (Aug 21, 2023)
12-123194492-C-T		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPHOSPH9	protein_coding	protein_coding	ENST00000392425	20	91695

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.66e-10	1.00	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	494	544	0.909	0.0000289	6750
Missense in Polyphen		137	172.69	0.79334		2242
Synonymous	1.42	171	196	0.871	0.0000111	1929
Loss of Function	3.71	26	56.0	0.464	0.00000308	696

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000525	0.000525
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.000111	0.000109
South Asian	0.000329	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• loftool: 0.894
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.74

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.273
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0253

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mphosph9

Gene ontology

• Cellular component: Golgi membrane;Golgi apparatus;centriole;membrane