TOMM5

translocase of outer mitochondrial membrane 5, the group of Translocase of outer mitochondrial membrane complex

Basic information

Region (hg38): 9:37582646-37592604

Previous symbols: [ "C9orf105" ]

Links

ENSG00000175768 ∙ NCBI:401505 ∙ OMIM:616169 ∙ HGNC:31369 ∙ Uniprot:Q8N4H5 ∙ 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 TOMM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM5 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	5	1	0

Variants in TOMM5

This is a list of pathogenic ClinVar variants found in the TOMM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-37592265-A-G		not specified	Uncertain significance (May 26, 2022)
9-37592267-A-G		not specified	Uncertain significance (Mar 28, 2022)
9-37592298-G-C		not specified	Uncertain significance (Jun 26, 2023)
9-37592348-G-A		not specified	Uncertain significance (Dec 14, 2023)
9-37592354-G-A		not specified	Uncertain significance (Aug 31, 2022)
9-37592494-C-T			Likely benign (May 01, 2022)
9-37592502-G-T		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM5	protein_coding	protein_coding	ENST00000544379	1	9997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.500	0.433	124503	0	9	124512	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.324	50	56.9	0.879	0.00000254	582
Missense in Polyphen		11	11.175	0.98437		96
Synonymous	-0.141	26	25.1	1.04	0.00000114	198
Loss of Function	1.29	0	1.93	0.00	8.03e-8	25

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000161	0.000160
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.0000557	0.0000556
South Asian	0.00	0.00
Other	0.000497	0.000496

dbNSFP

Source: dbNSFP

• Pathway: Metabolism of proteins;Pink/Parkin Mediated Mitophagy;Mitophagy;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.0819

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.205
• hipred: N
• hipred_score: 0.187
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tomm5
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: protein targeting to mitochondrion
• Cellular component: mitochondrion;mitochondrial outer membrane;mitochondrial outer membrane translocase complex;integral component of membrane
• Molecular function: protein transporter activity