BMT2

base methyltransferase of 25S rRNA 2 homolog, the group of Seven-beta-strand methyltransferase motif containing

Basic information

Region (hg38): 7:112819147-112939875

Previous symbols: [ "C7orf60" ]

Links

ENSG00000164603 ∙ NCBI:154743 ∙ OMIM:617855 ∙ HGNC:26475 ∙ Uniprot:Q1RMZ1 ∙ 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 BMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BMT2 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in BMT2

This is a list of pathogenic ClinVar variants found in the BMT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-112939678-G-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BMT2	protein_coding	protein_coding	ENST00000297145	5	120770

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00254	124788	0	6	124794	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	124	215	0.576	0.0000103	2665
Missense in Polyphen		17	58.234	0.29193		729
Synonymous	0.0152	77	77.2	0.998	0.00000353	762
Loss of Function	3.88	0	17.5	0.00	8.97e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000952	0.0000939
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000568	0.0000556
Finnish	0.0000470	0.0000464
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.0000568	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-binding protein that acts as an inhibitor of mTORC1 signaling via interaction with the GATOR1 and KICSTOR complexes (PubMed:29123071). Acts as a sensor of S- adenosyl-L-methionine to signal methionine sufficiency to mTORC1: in presence of methionine, binds S-adenosyl-L-methionine, leading to disrupt interaction with the GATOR1 and KICSTOR complexes and promote mTORC1 signaling (PubMed:29123071). Upon methionine starvation, S-adenosyl-L-methionine levels are reduced, thereby promoting the association with GATOR1 and KICSTOR, leading to inhibit mTORC1 signaling (PubMed:29123071). Probably also acts as a S-adenosyl-L-methionine-dependent methyltransferase (Potential). {ECO:0000255|HAMAP-Rule:MF_03044, ECO:0000269|PubMed:29123071}.

Intolerance Scores

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.728
• ghis: 0.636

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Bmt2

Gene ontology

• Biological process: rRNA methylation;cellular response to amino acid starvation;negative regulation of TORC1 signaling
• Cellular component: nucleolus;KICSTOR complex;GATOR1 complex
• Molecular function: rRNA (adenine) methyltransferase activity;S-adenosyl-L-methionine binding