TOMM20

translocase of outer mitochondrial membrane 20, the group of Small nucleolar RNA protein coding host genes|Translocase of outer mitochondrial membrane complex

Basic information

Region (hg38): 1:235109341-235128837

Links

ENSG00000173726

∙ NCBI:9804 ∙ OMIM:601848 ∙ HGNC:20947 ∙ Uniprot:Q15388 ∙ 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 TOMM20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM20 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 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	1	0	1

Variants in TOMM20

This is a list of pathogenic ClinVar variants found in the TOMM20 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-235109879-T-C			Benign (Feb 18, 2020)	1181185
1-235112077-T-C		not specified	Uncertain significance (Feb 16, 2023)	2486015

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM20	protein_coding	protein_coding	ENST00000366607	5	19601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0267	0.925	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	37	75.5	0.490	0.00000332	940
Missense in Polyphen		4	13.253	0.30181		177
Synonymous	0.172	27	28.2	0.959	0.00000130	276
Loss of Function	1.70	4	9.71	0.412	4.42e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Central component of the receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore (By similarity). {ECO:0000250}.;
Pathway: Post-translational protein modification;Metabolism of proteins;Pink/Parkin Mediated Mitophagy;Mitophagy;Ub-specific processing proteases;Deubiquitination;Mitochondrial protein import (Consensus)

Recessive Scores

pRec: 0.119

Intolerance Scores

loftool: 0.426
rvis_EVS: 0.08
rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

pHI: 0.305
hipred: Y
hipred_score: 0.853
ghis: 0.628

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.988

Mouse Genome Informatics

Gene name: Tomm20
Phenotype

Gene ontology

Biological process: protein targeting to mitochondrion;response to muscle activity;tRNA import into mitochondrion;protein deubiquitination;protein import into mitochondrial matrix;mitochondrial outer membrane translocase complex assembly;response to 3,3',5-triiodo-L-thyronine
Cellular component: mitochondrion;mitochondrial outer membrane;mitochondrial outer membrane translocase complex;integral component of mitochondrial outer membrane;mitochondria-associated endoplasmic reticulum membrane
Molecular function: protein binding;protein transmembrane transporter activity;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;mitochondrion targeting sequence binding;unfolded protein binding