TOMM70

translocase of outer mitochondrial membrane 70, the group of Translocase of outer mitochondrial membrane complex|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 3:100363431-100401089

Previous symbols: [ "TOMM70A" ]

Links

ENSG00000154174 ∙ NCBI:9868 ∙ OMIM:606081 ∙ HGNC:11985 ∙ Uniprot:O94826 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nervous system disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TOMM70 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM70 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			8	1		9
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	1

Variants in TOMM70

This is a list of pathogenic ClinVar variants found in the TOMM70 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-100365571-G-A		TOMM70-related neurodevelopmental disorder	Uncertain significance (Jan 10, 2020)
3-100365607-G-C		Inborn genetic diseases	Uncertain significance (Oct 18, 2021)
3-100365646-G-A			Uncertain significance (Nov 24, 2020)
3-100368105-T-C		See cases	Likely benign (Jan 05, 2021)
3-100369111-CA-C		See cases	Uncertain significance (Jan 06, 2021)
3-100372691-G-A		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
3-100372706-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2021)
3-100375052-G-A		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
3-100377715-G-C		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
3-100377852-A-G			Benign (Apr 06, 2018)
3-100381705-G-A			Uncertain significance (Nov 25, 2020)
3-100386810-G-A		TOMM70-related neurodevelopmental disorder	Uncertain significance (Jan 03, 2022)
3-100400720-A-C		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
3-100400828-A-C		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM70	protein_coding	protein_coding	ENST00000284320	12	37968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00159	125662	0	56	125718	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.92	221	317	0.697	0.0000152	3983
Missense in Polyphen		55	115.42	0.47652		1405
Synonymous	0.861	106	118	0.899	0.00000607	1125
Loss of Function	4.75	3	32.0	0.0937	0.00000160	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00135
Ashkenazi Jewish	0.000199	0.0000992
East Asian	0.000110	0.000109
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000240	0.000237
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor that accelerates the import of all mitochondrial precursor proteins. {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: 0.130

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.492
• hipred: Y
• hipred_score: 0.786
• ghis: 0.674

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Tomm70a

Zebrafish Information Network

• Gene name: tomm70a
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

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