MDN1

protein-coding

midasin AAA ATPase 1, the group of AAA ATPases

Gene summary

Predicted to enable ATP hydrolysis activity. Involved in ribosomal large subunit assembly. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014611.3

Inheritance

—

ClinVar variants

U:775B:116

Top phenotype

MDN1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr6:89,642,498-89,819,794

External References & Databases

Ensembl (ENSG00000112159)

Transcript & Mutation Effects

hg38 • Region Span ~177.3 kb

Loading mutation effect viewer...

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 MDN1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 756

MDN1-related disorderTotal: 100

not providedTotal: 22

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014611.3. 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			8 clinvar	26 clinvar	15 clinvar	49
missense			748 clinvar	58 clinvar	17 clinvar	823
nonsense			6 clinvar			6
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			12 clinvar			12
Total	0	0	775	84	32	891

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014611.3	RefSeq	NP_055426.1	102	MANE Select
ENST00000369393.8	Ensembl	ENSP00000358400.3	102	MANE Select
ENST00001112227.1	Ensembl	ENSP00000782032.1	23	Standard
ENST00001141594.1	Ensembl	ENSP00000809540.1	102	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
mdn1	Danio rerio	Structure: melanocyte Quality: quality abnormal

Gene / Model

Organism

Observed Phenotype

mdn1

Danio rerio

Structure: melanocyte

Quality: quality

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)

Biological Process

ribosomal large subunit assembly
rRNA processing
protein-containing complex assembly

Molecular Function

protein binding
ATP binding
ATPase activity
unfolded protein binding

Cellular Component

nucleus
nucleoplasm
nucleolus
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369393
Coding exons: 102
Length: 177225
Individuals with no LoFs: 125580
Homozygous LoFs: 0
Heterozygous LoFs: 168
Defined: 125748
p: 0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	2653	2.96e+3	0.896	0.000162	36739
Missense (PolyPhen)		588	758.57	0.77514		9546
Synonymous	0.390	1091	1.11e+3	0.985	0.0000595	10731
Loss of Function	11.8	78	298	0.262	0.0000160	3502

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00087	0.00086	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00060	0.00060	rare
Finnish	0.00079	0.00079	rare
European (Non-Finnish)	0.00082	0.00079	rare
South Asian	0.00070	0.00069	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits (PubMed:27814492). Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre- 60S particles from the nucleolus and then driving late pre-60S particles from the nucleus (By similarity). At an early stage in 60S maturation, mediates the dissociation of the PeBoW complex (PES1-BOP1-WDR12) from early pre-60S particles, rendering them competent for export from the nucleolus to the nucleoplasm (By similarity). Subsequently recruited to the nucleoplasmic particles through interaction with SUMO-conjugated PELP1 complex (PubMed:27814492). This binding is only possible if the 5S RNP at the central protuberance has undergone the rotation to complete its maturation (By similarity). {ECO:0000250|UniProtKB:Q12019, ECO:0000269|PubMed:27814492}.;

Recessive Scores

pRec: 0.0956

Intolerance Scores

LoFtool: 0.695
RVIS EVS: 0.59
RVIS percentile EVS: 82.52

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.745

Gene Damage Prediction

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