MDN1

midasin AAA ATPase 1, the group of AAA ATPases

Basic information

Region (hg38): 6:89642497-89819794

Links

ENSG00000112159 ∙ NCBI:23195 ∙ OMIM:618200 ∙ HGNC:18302 ∙ Uniprot:Q9NU22 ∙ 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 MDN1 gene.

• Inborn genetic diseases (190 variants)
• not provided (17 variants)
• MDN1-related condition (3 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MDN1 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				5	2	7
missense			178	16	4	198
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				2		2
non coding						0
Total	0	0	179	21	6

Variants in MDN1

This is a list of pathogenic ClinVar variants found in the MDN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-89644075-G-A		not specified	Uncertain significance (Mar 05, 2024)
6-89644076-C-T		not specified	Uncertain significance (Jun 09, 2022)
6-89644151-C-T		not specified	Uncertain significance (Sep 28, 2022)
6-89644193-C-G		not specified	Uncertain significance (Oct 18, 2021)
6-89645016-C-A		not specified	Uncertain significance (Nov 27, 2023)
6-89645070-G-A		MDN1-related disorder	Benign (Jun 14, 2019)
6-89646533-A-G		MDN1-related disorder	Benign (Mar 25, 2019)
6-89646573-C-G		not specified	Uncertain significance (Feb 03, 2022)
6-89648092-G-A		MDN1-related disorder	Benign (Mar 08, 2019)
6-89648093-T-C		not specified	Uncertain significance (Sep 22, 2023)
6-89650031-G-A		not specified	Uncertain significance (Dec 21, 2023)
6-89650175-C-T		not specified	Uncertain significance (Aug 30, 2022)
6-89650725-G-A		MDN1-related disorder	Likely benign (Jun 11, 2019)
6-89650763-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-89650840-A-G		MDN1-related disorder • not specified	Benign/Likely benign (Jun 10, 2021)
6-89652214-C-T		not specified	Likely benign (May 03, 2023)
6-89653036-T-C		not specified	Uncertain significance (Jan 03, 2024)
6-89653103-T-C		MDN1-related disorder	Likely benign (Jul 23, 2019)
6-89653113-T-G		MDN1-related disorder • not specified	Conflicting classifications of pathogenicity (Jul 06, 2022)
6-89653116-G-T		not specified	Uncertain significance (Nov 13, 2023)
6-89654154-C-T		MDN1-related disorder	Likely benign (Feb 07, 2020)
6-89654168-G-A			Likely benign (Mar 29, 2018)
6-89654214-A-G		not specified	Uncertain significance (Jan 19, 2022)
6-89654302-T-C		not specified	Uncertain significance (Sep 17, 2021)
6-89655791-T-G		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MDN1	protein_coding	protein_coding	ENST00000369393	102	177225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.16e-8	1.00	125580	0	168	125748	0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	2653	2.96e+3	0.896	0.000162	36739
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00113
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000601	0.000598
Finnish	0.000786	0.000786
European (Non-Finnish)	0.000823	0.000791
Middle Eastern	0.000601	0.000598
South Asian	0.000699	0.000686
Other	0.000655	0.000652

dbNSFP

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}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0956

Intolerance Scores

• loftool: 0.695
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.52

Haploinsufficiency Scores

• pHI: 0.368
• hipred: Y
• hipred_score: 0.550
• ghis: 0.572

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.745

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mdn1

Zebrafish Information Network

• Gene name: mdn1
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: ribosomal large subunit assembly;rRNA processing;protein-containing complex assembly
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;membrane;intermediate filament cytoskeleton
• Molecular function: protein binding;ATP binding;ATPase activity;unfolded protein binding