TOMM22

translocase of outer mitochondrial membrane 22, the group of Translocase of outer mitochondrial membrane complex

Basic information

Region (hg38): 22:38681957-38685421

Links

ENSG00000100216 ∙ NCBI:56993 ∙ OMIM:607046 ∙ HGNC:18002 ∙ Uniprot:Q9NS69 ∙ 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 TOMM22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM22 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in TOMM22

This is a list of pathogenic ClinVar variants found in the TOMM22 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-38682007-C-T		not specified	Uncertain significance (Nov 21, 2022)
22-38682018-C-G		not specified	Uncertain significance (Mar 25, 2024)
22-38682327-A-G		not specified	Uncertain significance (Aug 02, 2022)
22-38682387-C-T		not specified	Uncertain significance (May 03, 2023)
22-38682963-A-C		not specified	Uncertain significance (Oct 14, 2023)
22-38683810-G-A		not specified	Uncertain significance (Apr 27, 2023)
22-38683812-G-C		not specified	Uncertain significance (Feb 10, 2022)
22-38683816-T-C		not specified	Uncertain significance (Jan 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM22	protein_coding	protein_coding	ENST00000216034	4	2866

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.608	0.384	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.929	57	80.4	0.709	0.00000391	905
Missense in Polyphen		9	20.012	0.44973		238
Synonymous	-0.419	36	32.9	1.09	0.00000170	287
Loss of Function	2.14	1	7.19	0.139	3.07e-7	78

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)	0.0000181	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Central receptor component of the translocase of the outer membrane of mitochondria (TOM complex) responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with the peripheral receptor TOM20 functions as the transit peptide receptor and facilitates the movement of preproteins into the translocation pore. {ECO:0000269|PubMed:10982837}.
• Pathway: Metabolism of proteins;Pink/Parkin Mediated Mitophagy;Mitophagy;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.117
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.660
• ghis: 0.697

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tomm22

Zebrafish Information Network

• Gene name: tomm22
• Affected structure: cholangiocyte
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: protein targeting to mitochondrion;positive regulation of apoptotic process;protein insertion into mitochondrial outer membrane;protein insertion into mitochondrial membrane;protein transmembrane transport
• Cellular component: mitochondrion;mitochondrial outer membrane;mitochondrial outer membrane translocase complex;membrane;integral component of membrane
• Molecular function: protein binding;protein transmembrane transporter activity