TOMM40

translocase of outer mitochondrial membrane 40, the group of Translocase of outer mitochondrial membrane complex

Basic information

Region (hg38): 19:44890568-44903689

Links

ENSG00000130204 ∙ NCBI:10452 ∙ OMIM:608061 ∙ HGNC:18001 ∙ Uniprot:O96008 ∙ 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 TOMM40 gene.

• Inborn genetic diseases (15 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM40 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			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	2

Variants in TOMM40

This is a list of pathogenic ClinVar variants found in the TOMM40 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44891486-G-A		not specified	Uncertain significance (Oct 25, 2022)
19-44891543-G-C		not specified	Uncertain significance (Aug 13, 2021)
19-44891562-T-G			Benign (Jun 26, 2018)
19-44891608-G-C		not specified	Uncertain significance (Jun 28, 2022)
19-44891608-G-T		not specified	Uncertain significance (Aug 21, 2023)
19-44891639-G-T		not specified	Uncertain significance (Jan 31, 2024)
19-44891642-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-44892394-G-C			Likely benign (Apr 04, 2018)
19-44892864-A-G		not specified	Uncertain significance (Dec 12, 2023)
19-44892877-A-G		not specified	Uncertain significance (Mar 31, 2022)
19-44892904-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-44893781-C-T		not specified	Uncertain significance (Oct 18, 2021)
19-44894030-G-A		not specified	Uncertain significance (Dec 27, 2022)
19-44894057-G-A		not specified	Uncertain significance (Jun 26, 2023)
19-44900738-G-A		not specified	Uncertain significance (May 22, 2023)
19-44900743-C-T			Benign (Apr 10, 2018)
19-44900834-C-G		not specified	Uncertain significance (Jun 16, 2022)
19-44901208-C-T		not specified	Likely benign (Nov 21, 2023)
19-44901268-G-A		not specified	Uncertain significance (Jan 04, 2022)
19-44903042-G-A		not specified	Uncertain significance (Oct 27, 2022)
19-44903063-C-T		not specified	Uncertain significance (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM40	protein_coding	protein_coding	ENST00000426677	9	13121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00782	125691	0	1	125692	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	100	182	0.549	0.0000102	2294
Missense in Polyphen		13	44.099	0.29479		608
Synonymous	1.01	67	78.4	0.855	0.00000478	760
Loss of Function	3.53	0	14.5	0.00	6.19e-7	179

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)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Channel-forming protein essential for import of protein precursors into mitochondria. {ECO:0000269|PubMed:15644312}.
• Pathway: Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Metabolism of proteins;Pink/Parkin Mediated Mitophagy;Mitophagy;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.741
• hipred: Y
• hipred_score: 0.685
• ghis: 0.570

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tomm40

Gene ontology

• Biological process: protein targeting to mitochondrion;ion transport;protein import into mitochondrial matrix
• Cellular component: mitochondrion;mitochondrial outer membrane;mitochondrial outer membrane translocase complex;mitochondrial inner membrane;cytosol;integral component of membrane;integral component of mitochondrial outer membrane;pore complex
• Molecular function: protein binding;protein transmembrane transporter activity;porin activity