MPHOSPH6

protein-coding

M-phase phosphoprotein 6

Gene summary

Predicted to enable RNA binding activity. Involved in maturation of 5.8S rRNA. Located in nuclear exosome (RNase complex) and nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_005792.2

Inheritance

—

ClinVar variants

U:30B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr16:82,147,798-82,170,224

External References & Databases

Ensembl (ENSG00000135698)

Transcript & Mutation Effects

hg38 • Region Span ~22.4 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 MPHOSPH6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005792.2. 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			28 clinvar	1 clinvar	1 clinvar	30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	30	2	2	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005792.2	RefSeq	NP_005783.2	5	MANE Select
ENST00000258169.9	Ensembl	ENSP00000258169.4	5	MANE Select
ENST00000563100.5	Ensembl	ENSP00000454996.1	4	Standard
ENST00000563504.5	Ensembl	ENSP00000456626.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA degradation - Homo sapiens (human)

Biological Process

maturation of 5.8S rRNA
rRNA processing

Molecular Function

RNA binding
protein binding

Cellular Component

nuclear exosome (RNase complex)
exosome (RNase complex)
nucleus
nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258169
Coding exons: 5
Length: 22429
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125747
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.28	108	76.4	1.41	0.00000324	1061
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.741
RVIS EVS: 0.46
RVIS percentile EVS: 78.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.578

Gene Damage Prediction

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