TOM1L2

target of myb1 like 2 membrane trafficking protein

Basic information

Region (hg38): 17:17843507-17972422

Links

ENSG00000175662 ∙ NCBI:146691 ∙ OMIM:615519 ∙ HGNC:11984 ∙ Uniprot:Q6ZVM7 ∙ 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 TOM1L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOM1L2 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in TOM1L2

This is a list of pathogenic ClinVar variants found in the TOM1L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-17847639-A-C		not specified	Uncertain significance (Jun 10, 2024)
17-17847640-G-C		not specified	Uncertain significance (Sep 22, 2022)
17-17847678-C-T		not specified	Uncertain significance (Mar 21, 2023)
17-17847717-G-A		not specified	Uncertain significance (Aug 12, 2022)
17-17847733-C-T		not specified	Likely benign (Feb 28, 2023)
17-17848828-C-T		not specified	Uncertain significance (Sep 14, 2022)
17-17848831-G-T		not specified	Uncertain significance (Jan 12, 2024)
17-17848835-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-17848856-C-A		not specified	Uncertain significance (May 18, 2023)
17-17861489-T-C		not specified	Uncertain significance (May 11, 2022)
17-17861499-T-C		not specified	Uncertain significance (Nov 17, 2022)
17-17866341-T-C		not specified	Uncertain significance (Oct 05, 2021)
17-17866365-C-A		not specified	Uncertain significance (May 04, 2022)
17-17869344-C-G		not specified	Uncertain significance (Sep 27, 2022)
17-17869359-C-T		not specified	Uncertain significance (May 10, 2022)
17-17869395-C-T		not specified	Uncertain significance (Feb 22, 2024)
17-17869409-T-C		not specified	Uncertain significance (May 30, 2023)
17-17879657-C-G		not specified	Uncertain significance (Nov 07, 2023)
17-17879716-C-T		not specified	Uncertain significance (Jul 20, 2021)
17-17882781-G-A		not specified	Uncertain significance (Aug 02, 2022)
17-17882782-G-C		not specified	Uncertain significance (Feb 14, 2023)
17-17882784-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-17882823-G-A		not specified	Uncertain significance (Dec 11, 2023)
17-17884672-C-A		not specified	Uncertain significance (Jan 19, 2024)
17-17884678-T-C		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TOM1L2	protein_coding	protein_coding	ENST00000379504	15	128909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00157	0.998	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	280	314	0.892	0.0000187	3293
Missense in Polyphen		76	89.62	0.84802		971
Synonymous	-0.730	137	127	1.08	0.00000825	1024
Loss of Function	3.53	11	32.8	0.335	0.00000208	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000211
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable role in protein transport. May regulate growth factor-induced mitogenic signaling. {ECO:0000269|PubMed:16412388, ECO:0000269|PubMed:16479011}.
• Pathway: Fibroblast growth factor-1;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.547
• rvis_EVS: -1.16
• rvis_percentile_EVS: 6.17

Haploinsufficiency Scores

• pHI: 0.198
• hipred: Y
• hipred_score: 0.605
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.921

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tom1l2
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; reproductive system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: intracellular protein transport;signal transduction;negative regulation of mitotic nuclear division
• Cellular component: cell;extracellular exosome
• Molecular function: protein binding;protein kinase binding;clathrin binding