TOMM40L

translocase of outer mitochondrial membrane 40 like, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:161225938-161230746

Links

ENSG00000158882 ∙ NCBI:84134 ∙ ∙ HGNC:25756 ∙ Uniprot:Q969M1 ∙ 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 TOMM40L gene.

• Inborn genetic diseases (11 variants)
• not provided (4 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOMM40L 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	2	2	7
Total	0	0	13	2	2

Variants in TOMM40L

This is a list of pathogenic ClinVar variants found in the TOMM40L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161226953-C-A		not specified	Uncertain significance (Apr 07, 2022)
1-161227327-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-161227663-G-A		not specified	Uncertain significance (May 18, 2023)
1-161227684-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-161227695-G-C		not specified	Uncertain significance (May 27, 2022)
1-161227978-T-C		not specified	Uncertain significance (May 08, 2023)
1-161228225-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-161228815-G-C		not specified	Uncertain significance (Jul 12, 2023)
1-161228973-T-C		not specified	Uncertain significance (Apr 18, 2023)
1-161229055-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-161229087-G-A		not specified	Uncertain significance (Feb 10, 2022)
1-161229690-A-G			Likely benign (Jan 01, 2024)
1-161229713-G-A			Likely benign (Mar 01, 2022)
1-161229789-G-A		not specified	Benign (Sep 06, 2013)
1-161229790-C-A		TOMM40L-related disorder	Likely benign (Oct 30, 2019)
1-161229842-C-A			Uncertain significance (Mar 01, 2018)
1-161229865-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-161229866-G-A		not specified	Benign (Sep 25, 2015)
1-161229905-T-G			Uncertain significance (Dec 18, 2013)
1-161229914-C-T		not specified	Benign/Likely benign (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOMM40L	protein_coding	protein_coding	ENST00000367988	9	4616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.667	0.333	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	126	180	0.701	0.00000938	1983
Missense in Polyphen		39	68.75	0.56728		751
Synonymous	-0.390	74	69.8	1.06	0.00000365	627
Loss of Function	3.10	3	16.6	0.180	7.66e-7	178

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)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000663	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential channel-forming protein implicated in import of protein precursors into mitochondria. {ECO:0000250}.
• Pathway: Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.431
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.472
• hipred: Y
• hipred_score: 0.580
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.896

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tomm40l

Gene ontology

• Biological process: ion transport;biological_process;protein import into mitochondrial matrix
• Cellular component: mitochondrial outer membrane translocase complex;protein-containing complex;pore complex
• Molecular function: molecular_function;protein transmembrane transporter activity;porin activity;mitochondrion targeting sequence binding;preprotein binding