ETFBKMT

electron transfer flavoprotein subunit beta lysine methyltransferase, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 12:31647160-31673114

Previous symbols: [ "C12orf72", "METTL20" ]

Links

ENSG00000139160 ∙ NCBI:254013 ∙ OMIM:615256 ∙ HGNC:28739 ∙ Uniprot:Q8IXQ9 ∙ 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 ETFBKMT gene.

Variants pathogenicity by type

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

Variants in ETFBKMT

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

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

Position	Type	Phenotype	Significance	ClinVar
12-31662268-G-A			Likely benign (Mar 01, 2023)
12-31666126-T-C			Likely benign (Aug 01, 2022)
12-31667910-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETFBKMT	protein_coding	protein_coding	ENST00000357721	3	25955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.30e-9	0.0590	124625	11	1111	125747	0.00447

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.257	127	135	0.938	0.00000634	1720
Missense in Polyphen		49	47.017	1.0422		543
Synonymous	0.951	40	48.4	0.826	0.00000219	505
Loss of Function	-0.423	12	10.5	1.14	6.00e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00607	0.00607
Ashkenazi Jewish	0.00110	0.00109
East Asian	0.000272	0.000272
Finnish	0.0105	0.0103
European (Non-Finnish)	0.00474	0.00468
Middle Eastern	0.000272	0.000272
South Asian	0.00438	0.00439
Other	0.00523	0.00506

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase that selectively trimethylates the flavoprotein ETFB in mitochondria (PubMed:25023281, PubMed:25416781). Thereby, may negatively regulate the function of ETFB in electron transfer from Acyl-CoA dehydrogenases to the main respiratory chain (PubMed:25416781). {ECO:0000269|PubMed:25023281, ECO:0000269|PubMed:25416781}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.57

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.251
• ghis: 0.413

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Etfbkmt
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein methylation;peptidyl-lysine methylation;peptidyl-lysine trimethylation;negative regulation of electron transfer activity;negative regulation of fatty acid beta-oxidation using acyl-CoA dehydrogenase
• Cellular component: cytoplasm;mitochondrial matrix;protein-containing complex
• Molecular function: protein-lysine N-methyltransferase activity;heat shock protein binding