TOM1L2

gene
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Summary

TOM1L2 (target of myb1 like 2 membrane trafficking protein, HGNC:11984) is a protein-coding gene on chromosome 17p11.2, encoding TOM1-like protein 2 (Q6ZVM7). Acts as a MYO6/Myosin VI adapter protein that targets myosin VI to endocytic structures.

This gene belongs to a small gene family whose members have an N-terminal VHS domain followed by a GAT domain; domains which typically participate in vesicular trafficking. The canonical protein encoded by this gene also has a C-terminal clathrin binding motif. This protein has been shown to interact with Tollip, clathrin and ubiquitin and is thought to play a role in endosomal sorting. This gene resides in the 3.7 Mb deletion of chromosome region 17p11.2 that is associated with Smith-Magenis syndrome. Alternative splicing results in multiple transcript variants encoding distinct proteins.

Source: NCBI Gene 146691 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 89 total
  • MANE Select transcript: NM_001082968

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11984
Approved symbolTOM1L2
Nametarget of myb1 like 2 membrane trafficking protein
Location17p11.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000175662
Ensembl biotypeprotein_coding
OMIM615519
Entrez146691

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 35 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000318094, ENST00000379504, ENST00000395739, ENST00000468944, ENST00000478943, ENST00000486413, ENST00000535933, ENST00000537091, ENST00000540946, ENST00000542206, ENST00000577517, ENST00000577794, ENST00000579586, ENST00000581396, ENST00000890524, ENST00000890525, ENST00000890527, ENST00000890528, ENST00000890532, ENST00000890534, ENST00000890535, ENST00000890537, ENST00000890538, ENST00000890539, ENST00000890541, ENST00000890543, ENST00000890545, ENST00000890546, ENST00000890547, ENST00000890549, ENST00000890550, ENST00000890553, ENST00000890555, ENST00000890557, ENST00000890559, ENST00000890560, ENST00000890561, ENST00000950983, ENST00000950984

RefSeq mRNA: 9 — MANE Select: NM_001082968 NM_001033551, NM_001082968, NM_001288786, NM_001288787, NM_001288788, NM_001288789, NM_001350331, NM_001350332, NM_001350333

CCDS: CCDS32584, CCDS42270, CCDS74000, CCDS74001, CCDS74002, CCDS74003

Canonical transcript exons

ENST00000379504 — 15 exons

ExonStartEnd
ENSE000014813391789366117893810
ENSE000022087691797226217972400
ENSE000023741521786147617861551
ENSE000023897511786273117862848
ENSE000023902911785089317850952
ENSE000034625281789859617898674
ENSE000034770751786934017869473
ENSE000035166261786687617866924
ENSE000035551661786629617866419
ENSE000035586751787962717879743
ENSE000036101081788270517882863
ENSE000036292711790744717907531
ENSE000036350381784882317848859
ENSE000036766551788463417884768
ENSE000042822521784351117847783

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 97.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.8755 / max 159.9668, expressed in 1759 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
16480912.99461747
1648100.8810513

Top tissues by expression

287 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548897.88gold quality
apex of heartUBERON:000209897.86gold quality
right atrium auricular regionUBERON:000663196.79gold quality
heart left ventricleUBERON:000208496.56gold quality
right frontal lobeUBERON:000281096.54gold quality
lower esophagus mucosaUBERON:003583496.46gold quality
cardiac ventricleUBERON:000208296.40gold quality
cardiac atriumUBERON:000208196.20gold quality
tibial nerveUBERON:000132396.14gold quality
heartUBERON:000094895.56gold quality
right lobe of thyroid glandUBERON:000111995.55gold quality
lateral nuclear group of thalamusUBERON:000273695.51gold quality
skin of legUBERON:000151195.35gold quality
amygdalaUBERON:000187695.28gold quality
right hemisphere of cerebellumUBERON:001489095.19gold quality
left lobe of thyroid glandUBERON:000112095.10gold quality
substantia nigra pars reticulataUBERON:000196694.93gold quality
nucleus accumbensUBERON:000188294.90gold quality
thyroid glandUBERON:000204694.75gold quality
skin of abdomenUBERON:000141694.74gold quality
cingulate cortexUBERON:000302794.70gold quality
right coronary arteryUBERON:000162594.64gold quality
substantia nigra pars compactaUBERON:000196594.63gold quality
anterior cingulate cortexUBERON:000983594.61gold quality
cerebellar hemisphereUBERON:000224594.51gold quality
ventral tegmental areaUBERON:000269194.50gold quality
superior vestibular nucleusUBERON:000722794.49gold quality
trigeminal ganglionUBERON:000167594.46gold quality
cerebellar cortexUBERON:000212994.44gold quality
caudate nucleusUBERON:000187394.35gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

199 targeting TOM1L2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-4692100.0067.322066
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4673100.0066.641490
HSA-MIR-4283100.0066.422097
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4455100.0065.481587
HSA-MIR-453499.9966.581907
HSA-MIR-451499.9967.101870
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4645-5P99.9865.811284
HSA-MIR-569899.9768.492029
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-512-3P99.9767.351049
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-448799.9664.581252
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-185-3P99.9567.011743
HSA-MIR-808299.9567.271170
HSA-MIR-545-3P99.9570.742783
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-552-5P99.9368.561583
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-6783-3P99.8967.922059

Literature-anchored findings (GeneRIF, showing 3)

  • Two possible dementia susceptibility genes including ATPAF2 and TOM1L2 near SREBF1 locus were identified. (PMID:20167577)
  • Variants in the TOM1L2/SREBF1 locus exert opposing effects of total-body lean mass (TB-LM) and total-body less head bone mineral density (TBLH-BMD) . (PMID:28743860)
  • The ancestral ESCRT protein TOM1L2 selects ubiquitinated cargoes for retrieval from cilia. (PMID:37019113)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
danio_reriotom1l2ENSDARG00000009217
danio_rerioTOM1L2ENSDARG00000056394
mus_musculusTom1l2ENSMUSG00000000538
rattus_norvegicusTom1l2ENSRNOG00000003590
drosophila_melanogasterStamFBGN0027363
drosophila_melanogasterGgaFBGN0030141
drosophila_melanogasterWdfy2FBGN0032246
caenorhabditis_elegansstam-1WBGENE00004109
caenorhabditis_elegansWBGENE00008402

Paralogs (10): WDFY1 (ENSG00000085449), GGA1 (ENSG00000100083), TOM1 (ENSG00000100284), GGA2 (ENSG00000103365), STAM2 (ENSG00000115145), GGA3 (ENSG00000125447), STAM (ENSG00000136738), WDFY2 (ENSG00000139668), TOM1L1 (ENSG00000141198), HGS (ENSG00000185359)

Protein

Protein identifiers

TOM1-like protein 2Q6ZVM7 (reviewed: Q6ZVM7)

Alternative names: Target of Myb-like protein 2

All UniProt accessions (5): Q6ZVM7, B7Z2U2, F5H3S6, K7EKL6, K7ENB0

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a MYO6/Myosin VI adapter protein that targets myosin VI to endocytic structures. May also play a role in recruiting clathrin to endosomes. May regulate growth factor-induced mitogenic signaling.

Subunit / interactions. Interacts with clathrin, SRC and TOLLIP. Interacts with MYO6.

Tissue specificity. Ubiquitously expressed with higher expression in heart and skeletal muscle.

Domain organisation. The GAT domain mediates interaction with TOLLIP.

Similarity. Belongs to the TOM1 family.

Isoforms (5)

UniProt IDNamesCanonical?
Q6ZVM7-11yes
Q6ZVM7-22
Q6ZVM7-33
Q6ZVM7-44
Q6ZVM7-55

RefSeq proteins (9): NP_001028723, NP_001076437, NP_001275715, NP_001275716, NP_001275717, NP_001275718, NP_001337260, NP_001337261, NP_001337262 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002014VHS_domDomain
IPR004152GAT_domDomain
IPR008942ENTH_VHSHomologous_superfamily
IPR014645TOM1Family
IPR027429TOM1L2_VHS_domDomain
IPR038425GAT_sfHomologous_superfamily

Pfam: PF00790, PF03127

UniProt features (22 total): sequence conflict 8, splice variant 5, domain 2, region of interest 2, modified residue 2, chain 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ZVM7-F171.130.45

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 160, 164

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 208 (showing top): GOBP_REGULATION_OF_NUCLEAR_DIVISION, XU_GH1_AUTOCRINE_TARGETS_UP, GOZGIT_ESR1_TARGETS_DN, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, RICKMAN_METASTASIS_DN, GOBP_ORGANELLE_FISSION, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE, USF_01, GOBP_MITOTIC_NUCLEAR_DIVISION, HNF4_DR1_Q3, HFH4_01, GOBP_NEGATIVE_REGULATION_OF_MITOTIC_CELL_CYCLE, PPAR_DR1_Q2

GO Biological Process (3): signal transduction (GO:0007165), protein transport (GO:0015031), negative regulation of mitotic nuclear division (GO:0045839)

GO Molecular Function (5): protein kinase binding (GO:0019901), clathrin binding (GO:0030276), phosphatidylinositol binding (GO:0035091), ubiquitin binding (GO:0043130), protein binding (GO:0005515)

GO Cellular Component (3): endosome (GO:0005768), membrane (GO:0016020), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
transport1
intracellular protein localization1
establishment of protein localization1
regulation of mitotic nuclear division1
negative regulation of cell cycle process1
negative regulation of mitotic cell cycle1
negative regulation of nuclear division1
mitotic nuclear division1
kinase binding1
protein binding1
anion binding1
ubiquitin-like protein binding1
binding1
endomembrane system1
cytoplasmic vesicle1
cellular anatomical structure1
extracellular vesicle1

Protein interactions and networks

STRING

1004 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TOM1L2ZFYVE16Q7Z3T8886
TOM1L2EEA1Q15075700
TOM1L2APPL1Q9UKG1615
TOM1L2LMTK2Q8IWU2534
TOM1L2DAB2P98082528
TOM1L2TOLLIPQ9H0E2500
TOM1L2ICA1LQ8NDH6467
TOM1L2RTF2Q9BY42461
TOM1L2SRCP12931433
TOM1L2MYO6Q9UM54426
TOM1L2GIPC1O14908387
TOM1L2SNX32Q86XE0376
TOM1L2SLCO6A1Q86UG4372
TOM1L2ATPAF2Q8N5M1372
TOM1L2DRG2P55039355

IntAct

55 interactions, top by confidence:

ABTypeScore
TOLLIPTOM1psi-mi:“MI:0914”(association)0.890
ARRDC3WWP2psi-mi:“MI:0914”(association)0.770
CFTRESYT2psi-mi:“MI:0914”(association)0.710
MYO6GIPC1psi-mi:“MI:0914”(association)0.690
MYO6TOM1L2psi-mi:“MI:0915”(physical association)0.610
MYO6TOM1psi-mi:“MI:0914”(association)0.530
TOM1L2NDUFA6psi-mi:“MI:0914”(association)0.530
CUEDC1TOM1psi-mi:“MI:0914”(association)0.530
CTLA4B4GALT5psi-mi:“MI:0914”(association)0.530
TMEM171B3GAT3psi-mi:“MI:0914”(association)0.530
TRIM10WIZpsi-mi:“MI:0914”(association)0.530
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
TOM1L2RNF11psi-mi:“MI:0915”(physical association)0.370
LAPTM5TOM1L2psi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
PRNPCARNS1psi-mi:“MI:0914”(association)0.350
PRNPWDR91psi-mi:“MI:0914”(association)0.350
repABLIM1psi-mi:“MI:0914”(association)0.350
CTBP1TAF15psi-mi:“MI:0914”(association)0.350
ESR1ARPC1Bpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
ITM2BILVBLpsi-mi:“MI:0914”(association)0.350
CALM1MYO1Cpsi-mi:“MI:0914”(association)0.350
CALM2MYO1Cpsi-mi:“MI:0914”(association)0.350

BioGRID (95): TOM1L2 (Biochemical Activity), AGL (Co-fractionation), TOM1L2 (Affinity Capture-MS), TOM1L2 (Biochemical Activity), CUEDC1 (Affinity Capture-MS), SZRD1 (Affinity Capture-MS), NDUFA6 (Affinity Capture-MS), TOM1L2 (Reconstituted Complex), TOM1L2 (Two-hybrid), TOM1L2 (Proximity Label-MS), TOM1L2 (Proximity Label-MS), TOM1L2 (Affinity Capture-MS), TOM1L2 (Affinity Capture-MS), TOM1L2 (Two-hybrid), FAM9B (Two-hybrid)

ESM2 similar proteins: A0A8C0TYJ0, A0A8I5ZNK2, A2AWA9, A6QQZ7, A8KBF6, O55047, O88506, O95747, P20936, P23727, P26450, P27986, P31016, P78352, Q08CW1, Q08E27, Q12959, Q15139, Q15700, Q1ECX4, Q28C55, Q5PYH5, Q5PYH6, Q5PYH7, Q5R372, Q5R495, Q5R685, Q5R6Y5, Q5RAN1, Q5RCW6, Q5SRX1, Q5T2T1, Q5U2Y3, Q5ZIL4, Q5ZMW5, Q62101, Q62108, Q62696, Q63622, Q68FK8

Diamond homologs: A0A0D1E015, A0JMD2, A1CEK1, A1DFN5, A1DFP5, A2QWA2, A3LX75, A4QTV1, A8QCE4, A8XJZ8, B0WAQ0, B3MT31, B3P851, B4G2G5, B4IC49, B4JHI7, B4K982, B4M140, B4NFJ7, B4PRU6, E9Q4P1, F4KAU9, O12940, O13821, O14964, O60784, O76902, O88746, P0CR78, P0CR79, P0CS26, P0CS27, P38817, P40343, P87157, Q0CJU8, Q0CJV3, Q0P4S0, Q0U4Z8, Q0U6X7

SIGNOR signaling

1 interactions.

AEffectBMechanism
SMURF1unknownTOM1L2ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

89 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance76
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3412 predictions. Top by Δscore:

VariantEffectΔscore
17:17847780:AACT:Aacceptor_gain1.0000
17:17847781:ACTC:Aacceptor_loss1.0000
17:17847782:CT:Cacceptor_gain1.0000
17:17847783:TCTGC:Tacceptor_loss1.0000
17:17847784:C:CCacceptor_gain1.0000
17:17847784:CTGCA:Cacceptor_loss1.0000
17:17847785:T:Gacceptor_loss1.0000
17:17848648:T:TAdonor_gain1.0000
17:17848855:CCCTT:Cacceptor_gain1.0000
17:17848856:CCTTC:Cacceptor_gain1.0000
17:17862729:A:ACdonor_gain1.0000
17:17862730:C:CCdonor_gain1.0000
17:17862730:CGT:Cdonor_gain1.0000
17:17862732:T:TAdonor_gain1.0000
17:17866874:A:ACdonor_gain1.0000
17:17866874:ACT:Adonor_gain1.0000
17:17866875:C:CCdonor_gain1.0000
17:17866875:CT:Cdonor_gain1.0000
17:17866875:CTC:Cdonor_gain1.0000
17:17869336:CCACC:Cdonor_loss1.0000
17:17869337:CA:Cdonor_loss1.0000
17:17869339:C:Adonor_loss1.0000
17:17869339:CCT:Cdonor_gain1.0000
17:17879622:CTCA:Cdonor_loss1.0000
17:17879623:TCA:Tdonor_loss1.0000
17:17879624:CA:Cdonor_loss1.0000
17:17879744:C:CCacceptor_gain1.0000
17:17879755:C:CTacceptor_gain1.0000
17:17879755:C:Tacceptor_gain1.0000
17:17879757:C:CTacceptor_gain1.0000

AlphaMissense

3309 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:17869367:A:GL295P1.000
17:17869469:A:GL261P1.000
17:17884765:A:GW124R1.000
17:17884765:A:TW124R1.000
17:17847768:A:GL464P0.999
17:17847768:A:TL464H0.999
17:17847770:G:CF463L0.999
17:17847770:G:TF463L0.999
17:17847771:A:GF463S0.999
17:17847772:A:GF463L0.999
17:17847779:A:CF460L0.999
17:17847779:A:TF460L0.999
17:17847781:A:GF460L0.999
17:17869385:A:GL289P0.999
17:17869388:A:GL288P0.999
17:17869427:A:GL275P0.999
17:17879631:A:GL258P0.999
17:17879712:A:TV231D0.999
17:17884650:A:TI162K0.999
17:17884682:A:CF151L0.999
17:17884682:A:TF151L0.999
17:17884683:A:GF151S0.999
17:17884684:A:GF151L0.999
17:17884704:A:GL144P0.999
17:17893668:A:GL120P0.999
17:17893674:A:GL118P0.999
17:17893784:A:CC81W0.999
17:17893787:G:CN80K0.999
17:17893787:G:TN80K0.999
17:17893790:C:AK79N0.999

dbSNP variants (sampled 300 via entrez): RS1000016495 (17:17853739 G>A), RS1000030337 (17:17899858 A>C,T), RS1000031462 (17:17860009 C>A), RS1000038483 (17:17898531 G>A,C,T), RS1000056977 (17:17871434 C>T), RS1000065230 (17:17858528 G>A), RS1000095405 (17:17949598 G>A), RS1000096832 (17:17863807 C>T), RS1000099564 (17:17929065 G>A), RS1000147623 (17:17949906 T>C), RS1000164601 (17:17879803 A>G), RS1000181724 (17:17961137 C>T), RS1000182520 (17:17967778 T>A), RS1000194638 (17:17875899 T>C), RS1000222278 (17:17892267 C>T)

Disease associations

OMIM: gene MIM:615519 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

StudyTraitp-value
GCST002539_86Schizophrenia2.000000e-08
GCST004771_10TB-LM or TBLH-BMD (pleiotropy)1.000000e-10
GCST004946_149Schizophrenia7.000000e-10
GCST005348_40Total body bone mineral density2.000000e-11
GCST006803_40Schizophrenia3.000000e-08
GCST90020025_1401Waist-to-hip ratio adjusted for BMI1.000000e-09
GCST90020026_432Hip index1.000000e-09
GCST90020027_28Waist-hip index2.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004995lean body mass
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation5
Valproic Aciddecreases expression, increases expression, increases methylation3
sodium arsenitedecreases expression, increases abundance, increases expression, affects cotreatment2
Acetaminophendecreases expression, increases expression2
Arsenicdecreases expression, increases abundance, affects cotreatment2
Tretinoinincreases expression2
aristolochic acid Iincreases expression1
triphenyl phosphateaffects expression1
sodium arsenatedecreases expression, increases abundance1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, decreases expression1
trichostatin Aaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
manganese chloridedecreases expression, increases abundance1
polyhexamethyleneguanidineaffects expression1
CGP 52608affects binding, increases reaction1
bisphenol Bincreases expression1
abrineincreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases reaction, increases expression1
bisphenol Sdecreases methylation1
(+)-JQ1 compoundincreases expression1
Vehicle Emissionsdecreases reaction, increases expression1
Caffeinedecreases phosphorylation1
Dexamethasoneincreases expression1
Furaldehydeaffects cotreatment, affects localization, decreases expression1
Hydrogen Peroxideaffects expression1
Ivermectindecreases expression1
Manganesedecreases expression, increases abundance1
Potassium Dichromatedecreases expression1
Sodium Chlorideaffects cotreatment, affects localization, decreases expression1
Tobacco Smoke Pollutionincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.