TOM1

target of myb1 membrane trafficking protein, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 22:35299275-35347992

Links

ENSG00000100284 ∙ NCBI:10043 ∙ OMIM:604700 ∙ HGNC:11982 ∙ Uniprot:O60784 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immune system disorder (Limited), mode of inheritance: AD
• immunodeficiency 85 and autoimmunity (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 85 and autoimmunity	AD	Allergy/Immunology/Infectious	The condition can involve susceptibilty to infections, and awareness may allow preventative measures and early and aggressive treatment of infections; HSCT has been described	Allergy/Immunology/Infectious; Dermatologic	31263572

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TOM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOM1 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				2	3	5
missense			39	3	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2		1	3
non coding					4	4
Total	0	0	40	5	8

Variants in TOM1

This is a list of pathogenic ClinVar variants found in the TOM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-35299809-G-A		not specified	Benign (Jan 24, 2024)
22-35299978-T-G		not specified	Uncertain significance (Feb 15, 2023)
22-35300084-G-C		not specified	Benign (Jan 24, 2024)
22-35317869-C-A		not specified	Uncertain significance (Dec 17, 2022)
22-35317906-G-A		not specified	Uncertain significance (Jan 23, 2024)
22-35317938-C-T			Benign (Mar 01, 2018)
22-35317942-A-G		not specified	Uncertain significance (Apr 13, 2022)
22-35321953-C-T			Uncertain significance (Mar 01, 2024)
22-35321996-G-A		not specified	Uncertain significance (Feb 05, 2024)
22-35323062-G-A		not specified	Uncertain significance (Jun 07, 2024)
22-35323079-G-A		not specified	Uncertain significance (Jan 04, 2024)
22-35323167-A-G		not specified	Uncertain significance (Aug 23, 2021)
22-35323508-G-A		not specified	Uncertain significance (Jan 26, 2022)
22-35323526-G-A		not specified	Uncertain significance (May 23, 2023)
22-35323535-G-C		not specified	Uncertain significance (Jul 08, 2024)
22-35323541-G-T		not specified	Uncertain significance (Jun 27, 2023)
22-35323563-G-A		not specified	Uncertain significance (Dec 01, 2022)
22-35323626-A-G			Likely benign (Jul 01, 2022)
22-35323629-G-C			Uncertain significance (Jul 17, 2023)
22-35323771-G-A		not specified	Uncertain significance (Dec 27, 2023)
22-35323795-G-A		not specified	Uncertain significance (Dec 08, 2023)
22-35323853-C-G		not specified	Uncertain significance (May 20, 2024)
22-35323882-G-A		not specified	Likely benign (Apr 12, 2022)
22-35323894-A-G		not specified	Uncertain significance (Mar 15, 2024)
22-35327327-G-A			Benign (Aug 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOM1	protein_coding	protein_coding	ENST00000411850	15	48718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.45e-11	0.556	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	255	308	0.827	0.0000189	3193
Missense in Polyphen		105	136.84	0.76732		1462
Synonymous	1.02	120	135	0.888	0.00000937	1002
Loss of Function	1.38	21	29.0	0.724	0.00000161	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000322	0.000322
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000652	0.000653
South Asian	0.000262	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in intracellular trafficking. Probable association with membranes.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;EGFR1;C-MYB transcription factor network (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.884
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.8

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.743
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tom1

Gene ontology

• Biological process: intracellular protein transport;endocytosis;protein transport;endosomal transport;neutrophil degranulation
• Cellular component: cytoplasm;endosome;early endosome;cytosol;plasma membrane;membrane;azurophil granule membrane;specific granule membrane;extracellular exosome
• Molecular function: protein binding;clathrin binding