MAT2A

methionine adenosyltransferase 2A

Basic information

Region (hg38): 2:85539168-85545281

Links

ENSG00000168906

∙ NCBI:4144 ∙ OMIM:601468 ∙ HGNC:6904 ∙ Uniprot:P31153 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

familial thoracic aortic aneurysm and aortic dissection (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAT2A gene.

Familial_thoracic_aortic_aneurysm_and_aortic_dissection (180 variants)
Cardiovascular_phenotype (122 variants)
not_provided (28 variants)
not_specified (27 variants)
MAT2A-related_disorder (6 variants)
Isolated_thoracic_aortic_aneurysm (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAT2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005911.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	103 clinvar		104
missense	1 clinvar		73 clinvar	4 clinvar		78
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)				3 clinvar		3
Total	1	0	77	110	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAT2A	protein_coding	protein_coding	ENST00000306434	9	6116

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00154	125714	0	1	125715	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.63	69	221	0.312	0.0000114	2573
Missense in Polyphen		6	99.405	0.060359		1135
Synonymous	-0.816	83	74.1	1.12	0.00000359	771
Loss of Function	4.02	0	18.9	0.00	8.62e-7	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the formation of S-adenosylmethionine from methionine and ATP. The reaction comprises two steps that are both catalyzed by the same enzyme: formation of S-adenosylmethionine (AdoMet) and triphosphate, and subsequent hydrolysis of the triphosphate. {ECO:0000269|PubMed:10644686, ECO:0000269|PubMed:23189196, ECO:0000269|PubMed:25075345}.;
Pathway: Cysteine and methionine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Betaine Metabolism;Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;sarcosine oncometabolite pathway ;Spermidine and Spermine Biosynthesis;Selenoamino Acid Metabolism;Cystathionine Beta-Synthase Deficiency;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Trans-sulfuration and one carbon metabolism;Methionine De Novo and Salvage Pathway;One carbon metabolism and related pathways;Methylation Pathways;Methylation;Phase II - Conjugation of compounds;methionine degradation;Biological oxidations;Metabolism;Methionine Cysteine metabolism;Methionine and cysteine metabolism;Selenoamino acid metabolism;S-adenosyl-L-methionine biosynthesis;methionine salvage cycle III;C-MYB transcription factor network;cysteine biosynthesis;superpathway of methionine degradation (Consensus)

Recessive Scores

pRec: 0.315

Intolerance Scores

loftool: 0.143
rvis_EVS: -0.52
rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

pHI: 0.812
hipred: Y
hipred_score: 0.728
ghis: 0.652

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mat2a
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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype;

Zebrafish Information Network

Gene name: mat2aa
Affected structure: cardiac muscle cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: S-adenosylmethionine biosynthetic process;one-carbon metabolic process;protein hexamerization;protein heterooligomerization;cellular response to leukemia inhibitory factor
Cellular component: cytosol;methionine adenosyltransferase complex
Molecular function: methionine adenosyltransferase activity;protein binding;ATP binding;identical protein binding;metal ion binding