MAT2B

methionine adenosyltransferase 2 non-catalytic beta subunit, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 5:163503114-163519558

Links

ENSG00000038274

∙ NCBI:27430 ∙ OMIM:605527 ∙ HGNC:6905 ∙ Uniprot:Q9NZL9 ∙ 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 MAT2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAT2B 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						0
missense			13 clinvar		1 clinvar	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in MAT2B

This is a list of pathogenic ClinVar variants found in the MAT2B region.

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

Position	Phenotype	Significance	ClinVar
5-163505712-C-T	not specified	Uncertain significance (Oct 08, 2024)	3543613
5-163512093-A-G	not specified	Uncertain significance (Jul 05, 2024)	3543612
5-163512099-A-T	not specified	Uncertain significance (Mar 14, 2023)	2472983
5-163512101-G-A	not specified	Uncertain significance (Oct 25, 2023)	3123895
5-163512104-G-T	not specified	Uncertain significance (Sep 14, 2022)	2399055
5-163512112-T-G	not specified	Uncertain significance (Aug 02, 2022)	2304601
5-163513564-A-G	not specified	Uncertain significance (May 03, 2023)	2515278
5-163513950-A-G	not specified	Uncertain significance (Jun 18, 2021)	2233353
5-163516542-T-C	not specified	Uncertain significance (Feb 15, 2023)	2463573
5-163516563-A-C	not specified	Uncertain significance (Oct 28, 2024)	3543614
5-163516577-G-C	not specified	Uncertain significance (Oct 05, 2021)	3123896
5-163517591-T-G	not specified	Uncertain significance (Dec 05, 2022)	2332945
5-163517598-A-G	not specified	Uncertain significance (Jul 09, 2021)	2343984
5-163517635-T-G	not specified	Uncertain significance (Mar 07, 2024)	3123898
5-163518263-C-T		Benign (Dec 31, 2019)	717327
5-163518271-A-G	not specified	Uncertain significance (Jul 07, 2024)	3543615
5-163518293-G-A	not specified	Uncertain significance (May 26, 2022)	2363329
5-163518329-T-C	not specified	Uncertain significance (May 11, 2022)	2361520

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAT2B	protein_coding	protein_coding	ENST00000321757	7	16223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0462	0.949	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	129	168	0.768	0.00000787	2195
Missense in Polyphen		30	61.925	0.48446		766
Synonymous	-1.57	74	58.7	1.26	0.00000273	639
Loss of Function	2.47	5	15.5	0.322	8.19e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Regulatory subunit of S-adenosylmethionine synthetase 2, an enzyme that catalyzes the formation of S-adenosylmethionine from methionine and ATP. Regulates MAT2A catalytic activity by changing its kinetic properties, increasing its affinity for L- methionine (PubMed:10644686, PubMed:23189196, PubMed:25075345). Can bind NADP (in vitro) (PubMed:23189196, PubMed:23425511). {ECO:0000269|PubMed:10644686, ECO:0000269|PubMed:23189196, ECO:0000269|PubMed:23425511, 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;Trans-sulfuration pathway;One Carbon Metabolism;Trans-sulfuration and one carbon metabolism;Methionine De Novo and Salvage Pathway;Methylation Pathways;Methylation;Phase II - Conjugation of compounds;Post-translational protein modification;Metabolism of proteins;methionine degradation;Biological oxidations;Metabolism;Methionine Cysteine metabolism;Methionine and cysteine metabolism;Selenoamino acid metabolism;Ub-specific processing proteases;Deubiquitination;S-adenosyl-L-methionine biosynthesis;methionine salvage cycle III;cysteine biosynthesis;superpathway of methionine degradation (Consensus)

Recessive Scores

pRec: 0.292

Intolerance Scores

loftool: 0.397
rvis_EVS: -0.34
rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

pHI: 0.762
hipred: Y
hipred_score: 0.654
ghis: 0.631

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mat2b
Phenotype

Gene ontology

Biological process: S-adenosylmethionine biosynthetic process;one-carbon metabolic process;regulation of catalytic activity
Cellular component: nucleus;cytosol;methionine adenosyltransferase complex;extracellular exosome
Molecular function: protein binding;enzyme binding;methionine adenosyltransferase regulator activity