TOMM20L

translocase of outer mitochondrial membrane 20 like

Basic information

Region (hg38): 14:58395927-58408702

Links

ENSG00000196860 ∙ NCBI:387990 ∙ ∙ HGNC:33752 ∙ Uniprot:Q6UXN7 ∙ 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 TOMM20L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM20L 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in TOMM20L

This is a list of pathogenic ClinVar variants found in the TOMM20L region.

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

Position	Type	Phenotype	Significance	ClinVar
14-58395982-C-G		not specified	Likely benign (Mar 23, 2022)
14-58396023-C-G		not specified	Uncertain significance (Mar 07, 2024)
14-58396045-A-G		not specified	Likely benign (Mar 18, 2024)
14-58396057-C-G		not specified	Uncertain significance (Nov 30, 2021)
14-58396061-G-A		not specified	Uncertain significance (Jun 24, 2022)
14-58396304-G-A		not specified	Uncertain significance (Mar 16, 2022)
14-58402695-A-G		not specified	Uncertain significance (Mar 24, 2023)
14-58402734-C-T		not specified	Uncertain significance (Oct 12, 2022)
14-58407329-A-C		not specified	Uncertain significance (Mar 18, 2024)
14-58407343-A-T		not specified	Uncertain significance (Oct 06, 2021)
14-58407351-C-A		not specified	Uncertain significance (Apr 09, 2024)
14-58407376-G-A		not specified	Uncertain significance (May 20, 2024)
14-58407450-A-T		not specified	Uncertain significance (Mar 18, 2024)
14-58408574-C-A		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM20L	protein_coding	protein_coding	ENST00000360945	5	12786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000506	0.448	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.791	58	77.6	0.747	0.00000402	975
Missense in Polyphen		14	17.422	0.80358		223
Synonymous	-0.345	33	30.6	1.08	0.00000159	281
Loss of Function	0.363	7	8.11	0.863	3.42e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000662	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000662	0.000653
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0614

Intolerance Scores

• loftool: 0.733
• rvis_EVS: 0.48
• rvis_percentile_EVS: 78.95

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tomm20l
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: tRNA import into mitochondrion;protein import into mitochondrial matrix;mitochondrial outer membrane translocase complex assembly
• Cellular component: mitochondrial outer membrane translocase complex;integral component of mitochondrial outer membrane
• Molecular function: protein transmembrane transporter activity;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;mitochondrion targeting sequence binding