MN1

MN1 proto-oncogene, transcriptional regulator

Basic information

Region (hg38): 22:27748277-27801756

Previous symbols: [ "MGCR" ]

Links

ENSG00000169184 ∙ NCBI:4330 ∙ OMIM:156100 ∙ HGNC:7180 ∙ Uniprot:Q10571 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial meningioma (Limited), mode of inheritance: AD
• CEBALID syndrome (Strong), mode of inheritance: AD
• CEBALID syndrome (Strong), mode of inheritance: AD
• CEBALID syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Craniofacial defects, dysmorphic ears, structural brain abnormalities, expressive language delay, and impaired intellectual development (CEBALID syndrome); Meningioma, familial	AD	Audiologic/Otolaryngologic; Oncologic	CEBALID syndrome may include early-onset hearing loss among other features, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Meningomia, familial, surveillance for neoplasms to enable early treatment may improve outcomes	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic	2014801; 7731706; 31834374; 31839203

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MN1 gene.

• CEBALID syndrome (5 variants)
• MN1 C-terminal truncation (MCTT) syndrome (1 variants)
• not provided (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MN1 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			1	28	6	35
missense		1	128	20	1	150
nonsense	5	5				10
start loss						0
frameshift	1	2	5			8
inframe indel			5	9	3	17
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					6	6
Total	6	8	139	57	16

Variants in MN1

This is a list of pathogenic ClinVar variants found in the MN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-27750780-A-AG			Benign (May 13, 2021)
22-27750781-GA-G			Benign (May 23, 2021)
22-27750781-G-GA			Benign (May 16, 2021)
22-27750782-A-G			Benign (May 13, 2021)
22-27750925-G-T		CEBALID syndrome	Likely pathogenic (Feb 02, 2022)
22-27750935-A-G			Uncertain significance (May 17, 2023)
22-27750959-C-T		Inborn genetic diseases	Likely benign (Jan 07, 2022)
22-27750975-C-T		CEBALID syndrome • MN1 C-terminal truncation (MCTT) syndrome • Familial meningioma	Conflicting classifications of pathogenicity (Mar 01, 2024)
22-27750977-AG-A		CEBALID syndrome	Pathogenic (Apr 03, 2020)
22-27750980-T-C		Inborn genetic diseases	Uncertain significance (Nov 20, 2020)
22-27750983-G-GCA		MN1 C-terminal truncation (MCTT) syndrome	Likely pathogenic (-)
22-27750986-C-T		Inborn genetic diseases	Uncertain significance (Mar 31, 2022)
22-27750995-G-A		Inborn genetic diseases • not specified • CEBALID syndrome • MN1 C-terminal truncation (MCTT) syndrome	Pathogenic/Likely pathogenic (Sep 02, 2022)
22-27750997-G-T		Inborn genetic diseases	Uncertain significance (May 30, 2024)
22-27750998-C-CCTTGGCGTCA		CEBALID syndrome • MN1 C-terminal truncation (MCTT) syndrome	Pathogenic/Likely pathogenic (Feb 14, 2020)
22-27751005-G-A			Likely benign (May 01, 2024)
22-27751013-C-T		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)
22-27751028-GG-T		MN1 C-terminal truncation (MCTT) syndrome	Likely pathogenic (-)
22-27751028-GGACA-G		CEBALID syndrome	Pathogenic (Feb 14, 2020)
22-27751029-G-A		MN1-related disorder	Likely benign (Nov 19, 2019)
22-27751038-GC-G		Atrial septal defect;Congenital diaphragmatic hernia • MN1 C-terminal truncation (MCTT) syndrome	Uncertain significance (Dec 06, 2018)
22-27751043-G-A		CEBALID syndrome	Pathogenic (Jul 29, 2020)
22-27751055-CA-C		CEBALID syndrome	Likely pathogenic (Nov 03, 2022)
22-27751061-G-A		CEBALID syndrome • MN1 C-terminal truncation (MCTT) syndrome	Pathogenic (Nov 22, 2022)
22-27751063-G-A		Inborn genetic diseases	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MN1	protein_coding	protein_coding	ENST00000302326	2	53222

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000528	124769	0	3	124772	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	592	759	0.780	0.0000462	8365
Missense in Polyphen		220	292.4	0.7524		3382
Synonymous	1.30	335	367	0.914	0.0000276	2742
Loss of Function	5.41	0	34.0	0.00	0.00000158	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000556
Finnish	0.0000488	0.0000464
European (Non-Finnish)	0.00000884	0.00000883
Middle Eastern	0.0000560	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator which specifically regulates expression of TBX22 in the posterior region of the developing palate. Required during later stages of palate development for growth and medial fusion of the palatal shelves. Promotes maturation and normal function of calvarial osteoblasts, including expression of the osteoclastogenic cytokine TNFSF11/RANKL. Necessary for normal development of the membranous bones of the skull (By similarity). May play a role in tumor suppression (Probable). {ECO:0000250|UniProtKB:D3YWE6, ECO:0000305|PubMed:7731706}.
• Disease: DISEASE: Note=A chromosomal aberration involving MN1 may be a cause of acute myeloid leukemia (AML). Translocation t(12;22)(p13;q11) with ETV6. {ECO:0000269|PubMed:7731705}.; DISEASE: Note=Defects in MN1 involved in the development of meningiomas, slowly growing benign tumors derived from the arachnoidal cap cells of the leptomeninges, the soft coverings of the brain and spinal cord. Meningiomas are believed to be the most common primary tumors of the central nervous system in man. {ECO:0000269|PubMed:7731706}.

Haploinsufficiency Scores

• pHI: 0.291
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.179

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mn1
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: intramembranous ossification;regulation of transcription, DNA-templated;multicellular organism development;biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function