MNT

protein-coding

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

Gene summary

The Myc/Max/Mad network comprises a group of transcription factors that co-interact to regulate gene-specific transcriptional activation or repression. This gene encodes a protein member of the Myc/Max/Mad network. This protein has a basic-Helix-Loop-Helix-zipper domain (bHLHzip) with which it binds the canonical DNA sequence CANNTG, known as the E box, following heterodimerization with Max proteins. This protein is likely a transcriptional repressor and an antagonist of Myc-dependent transcriptional activation and cell growth. This protein represses transcription by binding to DNA binding proteins at its N-terminal Sin3-interaction domain. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020310.3

Inheritance

—

ClinVar variants

U:84B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:2,384,073-2,401,104

External References & Databases

Ensembl (ENSG00000070444)

Transcript & Mutation Effects

hg38 • Region Span ~17.0 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 MNT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020310.3. 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			2 clinvar	2 clinvar	2 clinvar	6
missense			79 clinvar	1 clinvar		80
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	84	3	2	89

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020310.3	RefSeq	NP_064706.1	6	MANE Select
ENST00000174618.5	Ensembl	ENSP00000174618.4	6	MANE Select
ENST00000575394.1	Ensembl	ENSP00000476269.1	2	Standard
ENST00000575394.2	Ensembl	ENSP00000476269.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

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

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000174618
Coding exons: 6
Length: 17059
Individuals with no LoFs: 125079
Homozygous LoFs: 0
Heterozygous LoFs: 195
Defined: 125274
p: 0.000779

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.981	283	333	0.849	0.0000198	3615
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0026	0.0025	notable
Latino/Admixed American	0.00066	0.00064	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00079	0.00076	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.00050	0.00050	rare
South Asian	0.0010	0.00098	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.891

Gene Damage Prediction

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