MGA

MAX dimerization protein MGA, the group of MAX dimerization proteins|MicroRNA protein coding host genes|T-box transcription factors

Basic information

Region (hg38): 15:41621134-41773081

Links

ENSG00000174197 ∙ NCBI:23269 ∙ OMIM:616061 ∙ HGNC:14010 ∙ Uniprot:Q8IWI9 ∙ 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 MGA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MGA 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	3	8
missense			19	6	5	30
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding					1	1
Total	0	0	19	12	9

Variants in MGA

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

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

Position	Type	Phenotype	Significance	ClinVar
15-41668993-T-C			Likely benign (Jul 01, 2023)
15-41669101-T-G		not specified	Uncertain significance (Aug 17, 2021)
15-41669728-C-A		not specified	Uncertain significance (Jun 18, 2021)
15-41669733-A-C		not specified	Uncertain significance (Aug 12, 2021)
15-41669882-C-G			Likely benign (Oct 01, 2020)
15-41669888-T-C		not specified	Uncertain significance (Jul 26, 2021)
15-41669906-A-G			Likely benign (Jun 01, 2018)
15-41696308-T-G		not specified	Uncertain significance (Nov 10, 2021)
15-41696511-A-G		not specified	Likely benign (Nov 09, 2021)
15-41696567-C-T			Likely benign (Feb 01, 2023)
15-41696827-C-T			Benign/Likely benign (Jul 01, 2023)
15-41697032-G-T			Benign (Mar 29, 2018)
15-41710806-T-A		not specified	Uncertain significance (Aug 12, 2021)
15-41711193-G-GCAGCAA			Likely benign (Dec 31, 2019)
15-41713282-C-T			Benign (Dec 31, 2019)
15-41727320-C-T		not specified	Uncertain significance (Oct 05, 2021)
15-41727351-A-G		not specified	Uncertain significance (Jun 22, 2021)
15-41727412-T-A			Benign (Dec 31, 2019)
15-41729188-G-A		not specified	Uncertain significance (Sep 15, 2021)
15-41729239-G-C		Multiple myeloma	Likely pathogenic (Aug 31, 2019)
15-41729256-C-T			Likely benign (Apr 01, 2023)
15-41736233-T-C			Likely benign (Dec 13, 2017)
15-41736499-C-G			Benign (Jun 27, 2018)
15-41736607-A-G			Benign (May 24, 2018)
15-41736622-A-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MGA	protein_coding	protein_coding	ENST00000219905	23	148720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.45e-16	124639	0	13	124652	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	1431	1.55e+3	0.921	0.0000792	19933
Missense in Polyphen		330	521.81	0.63241		6663
Synonymous	-0.111	564	561	1.01	0.0000274	6155
Loss of Function	9.58	5	117	0.0428	0.00000690	1480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000995	0.0000993
East Asian	0.00	0.00
Finnish	0.000101	0.0000928
European (Non-Finnish)	0.0000461	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.000131	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a dual-specificity transcription factor, regulating the expression of both MAX-network and T-box family target genes. Functions as a repressor or an activator. Binds to 5'-AATTTCACACCTAGGTGTGAAATT-3' core sequence and seems to regulate MYC-MAX target genes. Suppresses transcriptional activation by MYC and inhibits MYC-dependent cell transformation. Function activated by heterodimerization with MAX. This heterodimerization serves the dual function of both generating an E-box-binding heterodimer and simultaneously blocking interaction of a corepressor (By similarity). {ECO:0000250}.
• Pathway: Pathways Affected in Adenoid Cystic Carcinoma;Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.00847
• rvis_EVS: -0.61
• rvis_percentile_EVS: 17.48

Haploinsufficiency Scores

• pHI: 0.962
• hipred: Y
• hipred_score: 0.655
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mga
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; reproductive system 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); embryo phenotype

Zebrafish Information Network

• Gene name: mgaa
• Affected structure: forebrain midbrain boundary
• Phenotype tag: abnormal
• Phenotype quality: amorphous

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;negative regulation of G0 to G1 transition
• Cellular component: nucleoplasm;MLL1 complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;protein dimerization activity