MPHOSPH9

protein-coding

M-phase phosphoprotein 9

Gene summary

Involved in negative regulation of cilium assembly. Located in Golgi apparatus and microtubule organizing center. Implicated in multiple sclerosis. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_022782.4

Inheritance

—

ClinVar variants

U:157B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr12:123,152,320-123,244,014

External References & Databases

Ensembl (ENSG00000051825)

Transcript & Mutation Effects

hg38 • Region Span ~91.7 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 MPHOSPH9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 154

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022782.4. 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			1 clinvar	1 clinvar		2
missense			148 clinvar	8 clinvar		156
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	157	9	0	166

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022782.4	RefSeq	NP_073619.3	23	MANE Select
ENST00000606320.6	Ensembl	ENSP00000475489.1	23	MANE Select
ENST00000302373.8	Ensembl	ENSP00000304096.5	16	Standard
ENST00000535049.5	Ensembl	ENSP00000442663.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

Golgi membrane
Golgi apparatus
centriole
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392425
Coding exons: 20
Length: 91695
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.755	494	544	0.909	0.0000289	6750
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00027	0.00027	rare
South Asian	0.00033	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0891

Intolerance Scores

LoFtool: 0.894
RVIS EVS: -0.21
RVIS percentile EVS: 37.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0253

Gene Damage Prediction

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