TOM1L1

target of myb1 like 1 membrane trafficking protein

Basic information

Region (hg38): 17:54899386-54961956

Links

ENSG00000141198 ∙ NCBI:10040 ∙ OMIM:604701 ∙ HGNC:11983 ∙ Uniprot:O75674 ∙ 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 TOM1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOM1L1 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	21	2	0

Variants in TOM1L1

This is a list of pathogenic ClinVar variants found in the TOM1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-54900870-C-T		not specified	Uncertain significance (Dec 17, 2023)
17-54900884-C-T		not specified	Uncertain significance (Mar 20, 2023)
17-54900887-C-T		not specified	Uncertain significance (Mar 02, 2023)
17-54903757-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-54912677-G-C		not specified	Uncertain significance (Nov 30, 2022)
17-54912738-G-A		not specified	Uncertain significance (Aug 02, 2023)
17-54912747-G-A		not specified	Uncertain significance (Jun 10, 2024)
17-54912800-C-G		not specified	Uncertain significance (Mar 07, 2023)
17-54914650-C-G		not specified	Uncertain significance (Dec 05, 2022)
17-54914718-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-54915792-G-A		not specified	Uncertain significance (Sep 28, 2022)
17-54915803-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-54930092-G-A		not specified	Uncertain significance (May 23, 2023)
17-54937166-C-T		not specified	Uncertain significance (Aug 02, 2021)
17-54937167-G-A		not specified	Uncertain significance (Apr 11, 2023)
17-54937182-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-54937191-A-T		not specified	Uncertain significance (Mar 20, 2023)
17-54938956-A-C		not specified	Uncertain significance (Nov 29, 2023)
17-54938966-C-T		not specified	Uncertain significance (May 05, 2023)
17-54947301-G-A		not specified	Likely benign (Dec 28, 2022)
17-54947311-A-G		not specified	Likely benign (Nov 17, 2023)
17-54949575-G-C		not specified	Uncertain significance (Jun 21, 2022)
17-54950089-A-G		not specified	Uncertain significance (Jul 09, 2021)
17-54960583-T-C		not specified	Uncertain significance (Nov 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOM1L1	protein_coding	protein_coding	ENST00000575882	15	62563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.60e-10	0.810	125649	1	98	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.298	236	249	0.947	0.0000117	3155
Missense in Polyphen		82	83.869	0.97771		1162
Synonymous	1.70	69	89.5	0.771	0.00000456	875
Loss of Function	1.64	19	28.4	0.669	0.00000139	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000992	0.000930
Ashkenazi Jewish	0.00	0.00
East Asian	0.000657	0.000653
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000393	0.000387
Middle Eastern	0.000657	0.000653
South Asian	0.000528	0.000523
Other	0.000495	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable adapter protein involved in signaling pathways. Interacts with the SH2 and SH3 domains of various signaling proteins when it is phosphorylated. May promote FYN activation, possibly by disrupting intramolecular SH3-dependent interactions (By similarity). {ECO:0000250}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.0938

Intolerance Scores

• loftool: 0.914
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.542
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.643

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tom1l1

Gene ontology

• Biological process: intracellular protein transport;signal transduction;positive regulation of protein autophosphorylation;activation of protein kinase activity;ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway;negative regulation of mitotic nuclear division;regulation of DNA biosynthetic process
• Cellular component: cytoplasm;lysosome;endosome;Golgi stack;cytosol;endosome membrane;extracellular exosome
• Molecular function: protein binding;SH3 domain binding;protein kinase binding;clathrin binding;protein kinase activator activity;ubiquitin binding