MNT

MAX network transcriptional repressor, the group of MAX dimerization proteins|Basic helix-loop-helix proteins

Basic information

Region (hg38): 17:2384073-2401104

Links

ENSG00000070444 ∙ NCBI:4335 ∙ OMIM:603039 ∙ HGNC:7188 ∙ Uniprot:Q99583 ∙ 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 MNT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MNT 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				2	2	4
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	2

Variants in MNT

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

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

Position	Type	Phenotype	Significance	ClinVar
17-2386966-C-T		not specified	Uncertain significance (Jan 07, 2022)
17-2386992-T-C		not specified	Uncertain significance (Aug 11, 2024)
17-2387011-C-T		not specified	Uncertain significance (Mar 07, 2025)
17-2387050-C-T		not specified	Uncertain significance (Dec 14, 2024)
17-2387053-C-T		not specified	Uncertain significance (May 09, 2024)
17-2387055-G-A		not specified	Uncertain significance (Jun 05, 2024)
17-2387059-C-G		not specified	Uncertain significance (Apr 01, 2024)
17-2387101-C-T		not specified	Uncertain significance (Aug 19, 2024)
17-2387109-G-T		not specified	Uncertain significance (Jan 18, 2025)
17-2387111-C-T			Benign (Jul 16, 2018)
17-2387137-C-T		not specified	Uncertain significance (May 13, 2022)
17-2387164-C-A		not specified	Uncertain significance (Aug 01, 2024)
17-2387167-G-A		not specified	Uncertain significance (Nov 20, 2024)
17-2387188-T-C		not specified	Uncertain significance (Nov 06, 2023)
17-2387193-G-T		not specified	Uncertain significance (Oct 01, 2024)
17-2387194-G-A		not specified	Uncertain significance (Sep 14, 2023)
17-2387216-C-G			Likely benign (Jul 16, 2018)
17-2387403-G-A		not specified	Uncertain significance (Jun 02, 2024)
17-2387405-T-C			Likely benign (May 18, 2018)
17-2387467-G-A		not specified	Uncertain significance (May 15, 2024)
17-2387491-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-2387583-C-T		not specified	Uncertain significance (Aug 05, 2024)
17-2387589-T-A		not specified	Uncertain significance (Oct 09, 2024)
17-2387610-C-T		not specified	Likely benign (Aug 04, 2023)
17-2387916-C-A		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MNT	protein_coding	protein_coding	ENST00000174618	6	17059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00261	125079	0	195	125274	0.000779

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.981	283	333	0.849	0.0000198	3615
Missense in Polyphen		50	75.181	0.66507		836
Synonymous	-1.89	182	152	1.19	0.0000102	1295
Loss of Function	3.87	0	17.4	0.00	8.33e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00325	0.00313
Ashkenazi Jewish	0.000504	0.000498
East Asian	0.000790	0.000762
Finnish	0.00124	0.00120
European (Non-Finnish)	0.000504	0.000496
Middle Eastern	0.000790	0.000762
South Asian	0.00101	0.000981
Other	0.000333	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds DNA as a heterodimer with MAX and represses transcription. Binds to the canonical E box sequence 5'-CACGTG-3' and, with higher affinity, to 5'-CACGCG-3'.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.0396
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.393
• hipred: Y
• hipred_score: 0.748
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mnt
• Phenotype: skeleton phenotype; digestive/alimentary phenotype; neoplasm; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cellular phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;multicellular organism development;cell aging;negative regulation of cell population proliferation;regulation of cell cycle;positive regulation of nucleic acid-templated transcription;negative regulation of apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;transcription coactivator activity;transcription corepressor activity;protein dimerization activity