TOMM7

translocase of outer mitochondrial membrane 7, the group of Translocase of outer mitochondrial membrane complex

Basic information

Region (hg38): 7:22812628-22822849

Links

ENSG00000196683 ∙ NCBI:54543 ∙ OMIM:607980 ∙ HGNC:21648 ∙ Uniprot:Q9P0U1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Garg-Mishra progeroid syndrome (Limited), mode of inheritance: AR
• Garg-Mishra progeroid syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Garg-Mishra progeroid syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	36282599; 36299998

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TOMM7 gene.

• not_specified (8 variants)
• Garg-Mishra_progeroid_syndrome (2 variants)
• TOMM7-related_early_onset_Leigh_disease (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019059.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense	1	1	6			8
nonsense						0
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)			1			1
Total	2	1	7	0	0

Highest pathogenic variant AF is 0.00000805523

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM7	protein_coding	protein_coding	ENST00000358435	3	10220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00977	0.616	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.153	31	28.7	1.08	0.00000130	353
Missense in Polyphen		5	5.2373	0.95469		68
Synonymous	-1.96	18	10.1	1.79	5.16e-7	102
Loss of Function	0.336	3	3.70	0.811	1.57e-7	40

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)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for assembly and stability of the TOM complex. Positive regulator of PRKN translocation to damaged mitochondria. Acts probably by stabilizing PINK1 on the outer membrane of depolarized mitochondria. {ECO:0000269|PubMed:18331822, ECO:0000269|PubMed:24270810}.
• Pathway: Mitophagy - animal - Homo sapiens (human);Metabolism of proteins;Pink/Parkin Mediated Mitophagy;Mitophagy;Mitochondrial protein import (Consensus)

Intolerance Scores

• loftool: 0.474
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.0902
• hipred: N
• hipred_score: 0.435
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0314

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tomm7

Gene ontology

• Biological process: protein targeting to mitochondrion;protein import into mitochondrial matrix;regulation of protein stability;positive regulation of mitophagy in response to mitochondrial depolarization;positive regulation of protein targeting to mitochondrion
• Cellular component: mitochondrion;mitochondrial outer membrane;mitochondrial outer membrane translocase complex;integral component of membrane
• Molecular function: protein binding;protein transmembrane transporter activity