TOMM20

Summary

TOMM20 (translocase of outer mitochondrial membrane 20, HGNC:20947) is a protein-coding gene on chromosome 1q42.3, encoding Mitochondrial import receptor subunit TOM20 homolog (Q15388). Central receptor component of the translocase of the outer membrane of mitochondria (TOM) complex essential for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. It is a selective cancer dependency (DepMap: 87.0% of cell lines).

Enables mitochondrion targeting sequence binding activity; protein-transporting ATPase activity; and unfolded protein binding activity. Involved in protein targeting to mitochondrion. Located in mitochondria-associated endoplasmic reticulum membrane contact site and mitochondrial outer membrane. Is active in mitochondrion.

Source: NCBI Gene 9804 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 15 total
• Cancer dependency (DepMap): dependent in 87.0% of screened cell lines
• MANE Select transcript: NM_014765

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20947
Approved symbol	TOMM20
Name	translocase of outer mitochondrial membrane 20
Location	1q42.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0016, TOM20, MOM19, MAS20
Ensembl gene	ENSG00000173726
Ensembl biotype	protein_coding
OMIM	601848
Entrez	9804

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000366607, ENST00000467767, ENST00000473132, ENST00000898228, ENST00000932121, ENST00000932122, ENST00000932123

RefSeq mRNA: 1 — MANE Select: NM_014765 NM_014765

CCDS: CCDS1603

Canonical transcript exons

ENST00000366607 — 5 exons

Exon	Start	End
ENSE00001178159	235122326	235122372
ENSE00001442165	235109341	235112108
ENSE00001442166	235128595	235128837
ENSE00003482656	235113768	235113910
ENSE00003661254	235119818	235119899

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 151.3775 / max 956.5731, expressed in 1828 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18119	135.2109	1828
18118	9.3611	1788
18120	3.2629	1429
18121	1.7748	729
18122	1.7677	708

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	99.43	gold quality
upper leg skin	UBERON:0004262	99.35	gold quality
Brodmann (1909) area 10	UBERON:0013541	99.31	gold quality
frontal pole	UBERON:0002795	99.30	gold quality
cortical plate	UBERON:0005343	99.24	gold quality
skin of hip	UBERON:0001554	99.21	gold quality
middle frontal gyrus	UBERON:0002702	99.15	gold quality
caput epididymis	UBERON:0004358	99.08	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.03	gold quality
corpus epididymis	UBERON:0004359	98.97	gold quality
pons	UBERON:0000988	98.96	gold quality
orbitofrontal cortex	UBERON:0004167	98.91	gold quality
middle temporal gyrus	UBERON:0002771	98.86	gold quality
lateral globus pallidus	UBERON:0002476	98.81	gold quality
postcentral gyrus	UBERON:0002581	98.80	gold quality
adult organism	UBERON:0007023	98.76	gold quality
embryo	UBERON:0000922	98.75	gold quality
Brodmann (1909) area 46	UBERON:0006483	98.74	gold quality
parietal lobe	UBERON:0001872	98.73	gold quality
pigmented layer of retina	UBERON:0001782	98.71	gold quality
substantia nigra pars compacta	UBERON:0001965	98.69	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.64	gold quality
ganglionic eminence	UBERON:0004023	98.53	gold quality
blood vessel layer	UBERON:0004797	98.52	gold quality
parietal pleura	UBERON:0002400	98.50	gold quality
prefrontal cortex	UBERON:0000451	98.43	gold quality
superior vestibular nucleus	UBERON:0007227	98.43	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.43	gold quality
superior frontal gyrus	UBERON:0002661	98.40	gold quality
seminal vesicle	UBERON:0000998	98.37	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-7008	yes	915.21
E-MTAB-10042	yes	14.08
E-HCAD-31	no	21.54
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC, NFE2L2

miRNA regulators (miRDB)

147 targeting TOMM20, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 87.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 20)

• Tom34 unlike Tom20 does not interact with the leader sequences of mitochondrial precursor proteins (PMID:11913975)
• the cytosolic domains of Tom20 and Tom22 function to maintain their substrate preproteins unfolded and prevent them from aggregating on the mitochondrial surface (PMID:14699115)
• a novel model in which Tom20 binds Tom70 to facilitate preprotein release from the chaperones by competition (PMID:21771790)
• Tom20 was ubiquitously distributed in the organ of Corti, allowing well-delineated visualization of inner and outer hair cells. In the inner ear of aged subjects with Meniere’s disease, there was decreased expression of Tom20. (PMID:23165776)
• TOMM20 protein is highly expressed in both anaplastic thyroid cancer and papillary thyroid cancer compared to non-cancerous thyroid tissue. (PMID:26615136)
• Gsk3beta and Tomm20 are substrates of the SCFFbxo7/PARK15 ubiquitin ligase associated with Parkinson’s disease (PMID:27503909)
• TOMM20 and MCT1 were highly expressed in diffuse large B-cell lymphoma lymphocytes, indicating an OXPHOS phenotype, whereas non-neoplastic lymphocytes in the control samples did not express these markers. (PMID:29248132)
• TOMM20, MCT1, and MCT4 expression was significantly different in Hodgkin and Reed Sternberg (HRS) cells. HRS have high expression of TOMM20, while tumor associated macrophages have absent TOMM20 expression. Tumor-infiltrating lymphocytes have low TOMM20 expression. Reactive lymph nodes in contrast to cHL tumors had low TOMM20, MCT1, and MCT4 expression in lymphocytes and macrophages. (PMID:29248133)
• TOM70, but not TOM20, clusters in distinct OMM foci, frequently overlapping with sites in which the endoplasmic reticulum (ER) contacts mitochondria. Functionally, TOM70 depletion specifically impairs inositol trisphosphates (IP3)-linked ER to mitochondria Ca(2+) transfer. This phenomenon is dependent on the capacity of TOM70 to interact with IP3-receptors and favor their functional recruitment close to mitochondria. (PMID:29395920)
• Translocase of the outer mitochondrial membrane complex subunit 20 (TOMM20) facilitates cancer aggressiveness and therapeutic resistance in chondrosarcoma. (PMID:32920118)
• TOM20-mediated transfer of Bcl2 from ER to MAM and mitochondria upon induction of apoptosis. (PMID:33589622)
• The receptor subunit Tom20 is dynamically associated with the TOM complex in mitochondria of human cells. (PMID:34347503)
• Analysis of mitochondrial regulatory transcripts in publicly available datasets with validation in placentae from pre-term, post-term and fetal growth restriction pregnancies. (PMID:34364121)
• Structural basis of Tom20 and Tom22 cytosolic domains as the human TOM complex receptors. (PMID:35733257)
• Melatonin promoted osteogenesis of human periodontal ligament cells by regulating mitochondrial functions through the translocase of the outer mitochondrial membrane 20. (PMID:36373245)
• ATP13A2 modifies mitochondrial localization of overexpressed TOM20 to autolysosomal pathway. (PMID:36445873)
• TOMM20 as a Potential Prognostic Biomarker in Chordoma: Results From a High-Volume, Single-Center Study. (PMID:36857736)
• Iron induces B cell pyroptosis through Tom20-Bax-caspase-gasdermin E signaling to promote inflammation post-spinal cord injury. (PMID:37480037)
• AR antagonists develop drug resistance through TOMM20 autophagic degradation-promoted transformation to neuroendocrine prostate cancer. (PMID:37563661)
• Association of poly(rC)-binding protein-2 with sideroflexin-3 through TOM20 as an iron entry pathway to mitochondria. (PMID:38599240)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	tomm20a	ENSDARG00000103163
danio_rerio	tomm20b	ENSDARG00000103566
mus_musculus	Tomm20	ENSMUSG00000093904
rattus_norvegicus	Tomm20	ENSRNOG00000019980
drosophila_melanogaster	Tom20	FBGN0036928
drosophila_melanogaster	tomboy20	FBGN0037828
caenorhabditis_elegans		WBGENE00009092

Paralogs (1): TOMM20L (ENSG00000196860)

Protein

Protein identifiers

Mitochondrial import receptor subunit TOM20 homolog — Q15388 (reviewed: Q15388)

Alternative names: Mitochondrial 20 kDa outer membrane protein, Outer mitochondrial membrane receptor Tom20

All UniProt accessions (1): Q15388

UniProt curated annotations — full annotation on UniProt →

Function. Central receptor component of the translocase of the outer membrane of mitochondria (TOM) complex essential for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOMM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore. The TOM complex associates with the ion channel VDAC2 and PINK1 kinase at depolarized mitochondria, this interaction stabilizes PINK1 at the outer mitochondrial membrane and triggers downstream mitophagy by the recruitment of the E3 ubiquitin ligase PRKN. Required for the translocation across the mitochondrial outer membrane of cytochrome P450 monooxygenases.

Subunit / interactions. Part of the translocase of the outer mitochondrial membrane (TOM complex) consisting of at least TOMM5, TOMM6, TOMM7, TOMM20, TOMM22 and TOMM40. TOMM70 may also be found in the TOM complex. The TOM complex interacts with the VDAC2 homodimer. Upon mitochondrial depolarization, the TOM-VDAC assembly interacts with PINK1; the interaction stabilizes PINK1 at the outer mitochondrial membrane and triggers downstream mitophagy. Interacts with APEX1. Interacts with TBC1D21.

Subcellular location. Mitochondrion outer membrane.

Post-translational modifications. Ubiquitinated by PRKN during mitophagy, leading to its degradation and enhancement of mitophagy. Deubiquitinated by USP30.

Similarity. Belongs to the Tom20 family.

RefSeq proteins (1): NP_055580* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002056	MAS20	Family
IPR022422	MAS20_rcpt_metazoan	Family
IPR023392	Tom20_dom_sf	Homologous_superfamily

Pfam: PF02064

UniProt features (23 total): helix 7, cross-link 4, mutagenesis site 3, topological domain 2, sequence variant 2, modified residue 2, chain 1, sequence conflict 1, transmembrane region 1

Structure

Experimental structures (PDB)

12 structures.

PDB	Method	Resolution (Å)
4APO	X-RAY DIFFRACTION	1.9
7VBY	ELECTRON MICROSCOPY	2.54
9EII	ELECTRON MICROSCOPY	2.75
9EIH	ELECTRON MICROSCOPY	3.1
8UY3	X-RAY DIFFRACTION	3.2
9EIJ	ELECTRON MICROSCOPY	3.3
9JCE	ELECTRON MICROSCOPY	3.59
9J79	ELECTRON MICROSCOPY	4.08
9J7B	ELECTRON MICROSCOPY	4.12
9J7A	ELECTRON MICROSCOPY	4.13
8XVA	ELECTRON MICROSCOPY	5.92
7VC9	ELECTRON MICROSCOPY	13

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15388-F1	76.44	0.10

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 (6): 135, 138, 35, 56, 61, 68

Mutagenesis-validated functional residues (3):

Position	Phenotype
56	defects in mitophagy; when associated with r-61 and r-68.
61	defects in mitophagy; when associated with r-56 and r-68.
68	defects in mitophagy; when associated with r-56 and r-61.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-1268020	Mitochondrial protein import
R-HSA-5205685	PINK1-PRKN Mediated Mitophagy
R-HSA-5689880	Ub-specific processing proteases

MSigDB gene sets: 239 (showing top): GRUETZMANN_PANCREATIC_CANCER_DN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, SHEPARD_CRASH_AND_BURN_MUTANT_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_PROTEIN_TARGETING, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, NFKB_Q6, MODULE_239, WTGAAAT_UNKNOWN, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOCC_MITOCHONDRIAL_ENVELOPE, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN

GO Biological Process (7): obsolete protein targeting to mitochondrion (GO:0006626), intracellular protein transport (GO:0006886), tRNA import into mitochondrion (GO:0016031), protein import into mitochondrial matrix (GO:0030150), protein insertion into mitochondrial outer membrane (GO:0045040), protein targeting (GO:0006605), protein transport (GO:0015031)

GO Molecular Function (5): protein-transporting ATPase activity (GO:0015450), mitochondrion targeting sequence binding (GO:0030943), obsolete unfolded protein binding (GO:0051082), protein binding (GO:0005515), transmembrane protein transporter activity (GO:0008320)

GO Cellular Component (10): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), mitochondrial outer membrane translocase complex (GO:0005742), mitochondria-associated endoplasmic reticulum membrane contact site (GO:0044233), cell periphery (GO:0071944), sperm midpiece (GO:0097225), migrasome (GO:0140494), TOM complex (GO:0140596), mitochondrial envelope (GO:0005740), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Protein localization	1
Mitophagy	1
Deubiquitination	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
intracellular protein localization	2
establishment of protein localization	2
intracellular membrane-bounded organelle	2
protein transport	1
intracellular transport	1
RNA import into mitochondrion	1
tRNA transport	1
protein transmembrane import into intracellular organelle	1
protein localization to mitochondrion	1
import into the mitochondrion	1
mitochondrial protein import pathway	1
outer mitochondrial membrane organization	1
protein insertion into mitochondrial membrane	1
transport	1
transmembrane protein transporter activity	1
ATPase-coupled transmembrane transporter activity	1
signal sequence receptor activity	1
binding	1
macromolecule transmembrane transporter activity	1
protein transmembrane transport	1
protein transporter activity	1
cytoplasm	1
mitochondrial membrane	1
organelle outer membrane	1
outer mitochondrial membrane protein complex	1
organelle membrane contact site	1
sperm flagellum	1
mitochondrial outer membrane translocase complex	1
mitochondrion	1
organelle envelope	1

Protein interactions and networks

STRING

2994 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TOMM20	TOMM22	Q9NS69	999
TOMM20	TOMM70	O94826	999
TOMM20	TOMM40	O96008	999
TOMM20	TOMM7	Q9P0U1	996
TOMM20	TOMM5	Q8N4H5	992
TOMM20	TOMM6	Q96B49	988
TOMM20	SNCA	P37840	980
TOMM20	PINK1	Q9BXM7	934
TOMM20	TIMM23	O14925	932
TOMM20	TIMM17A	Q99595	922
TOMM20	SAMM50	Q9Y512	911
TOMM20	TIMM17B	O60830	850
TOMM20	MFN2	O95140	827
TOMM20	AIP	O00170	826
TOMM20	VDAC1	P21796	818

IntAct

60 interactions, top by confidence:

A	B	Type	Score
PINK1	PRKN	psi-mi:“MI:0403”(colocalization)	0.750
TOMM7	TOMM20	psi-mi:“MI:0915”(physical association)	0.560
VDAC1	HK1	psi-mi:“MI:0914”(association)	0.560
DYNLL1	BCL2L11	psi-mi:“MI:0915”(physical association)	0.500
TOMM20	TPP1	psi-mi:“MI:0914”(association)	0.480
TOMM20	PINK1	psi-mi:“MI:0403”(colocalization)	0.430
	TOMM20	psi-mi:“MI:0915”(physical association)	0.400
H1-5	TOMM20	psi-mi:“MI:0915”(physical association)	0.400
NFXL1	TOMM20	psi-mi:“MI:0915”(physical association)	0.400
SYNPO2L	TOMM20	psi-mi:“MI:0915”(physical association)	0.400
TOMM20	PABPC4	psi-mi:“MI:0915”(physical association)	0.400
ATXN1	TOMM20	psi-mi:“MI:0915”(physical association)	0.370
	TOMM20	psi-mi:“MI:0915”(physical association)	0.370
Nup155	AP3B1	psi-mi:“MI:0914”(association)	0.350
NCSTN	ESYT2	psi-mi:“MI:0914”(association)	0.350
Psmb5		psi-mi:“MI:0914”(association)	0.350
LIMA1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
NEDD1	ATP5MF-PTCD1	psi-mi:“MI:0914”(association)	0.350
ACTR5	TBRG1	psi-mi:“MI:0914”(association)	0.350
PML	ATP5MF-PTCD1	psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
MAPK6		psi-mi:“MI:0914”(association)	0.350
OCIAD1	NDUFS8	psi-mi:“MI:0914”(association)	0.350
FAF2	ERLIN1	psi-mi:“MI:0914”(association)	0.350
Synj2bp	STAT3	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (320): TOMM20 (Affinity Capture-RNA), TOMM20 (Affinity Capture-RNA), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS), SLC25A5 (Co-fractionation), SLC25A6 (Co-fractionation), TOMM20 (Synthetic Lethality), HSD17B10 (FRET), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS), TOMM20 (Affinity Capture-MS)

ESM2 similar proteins: A2AKQ8, A5PJZ5, A6H7B1, A8Y3V5, B2RYD6, O14225, O14579, O46563, O89079, P23231, P54729, Q0P4W3, Q15388, Q16891, Q19766, Q2UF96, Q4IBU4, Q4QQS2, Q4QR29, Q4X0I8, Q5AZQ5, Q5RA31, Q5RFR8, Q5ZIK9, Q62018, Q62760, Q66HC5, Q6DEU9, Q6DFM9, Q6DH66, Q6INU8, Q6NX12, Q6PD62, Q6WRS2, Q7S8M1, Q7ZU29, Q7ZX96, Q86WT1, Q8AVY0, Q8BJ71

Diamond homologs: A6H7B1, A8Y3V5, Q15388, Q19766, Q5RA31, Q62760, Q6DFM9, Q6DH66, Q6UXN7, Q8AVY0, Q9D4V6, Q9DCC8, O14225

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TOMM20	“form complex”	“TOM40 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
PINK1-PRKN Mediated Mitophagy	5	36.4×	9e-05
Mitochondrial protein import	5	17.1×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
ERAD pathway	6	17.5×	2e-04
regulation of apoptotic process	6	8.1×	3e-03
protein stabilization	7	7.5×	2e-03
regulation of cell cycle	6	7.2×	5e-03
intracellular protein transport	6	6.3×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

812 predictions. Top by Δscore:

Variant	Effect	Δscore
1:235113763:CTTA:C	donor_loss	1.0000
1:235113765:TACCT:T	donor_loss	1.0000
1:235113767:C:G	donor_loss	1.0000
1:235113767:CCTGA:C	donor_gain	1.0000
1:235113906:TTCAC:T	acceptor_gain	1.0000
1:235113907:TCACC:T	acceptor_loss	1.0000
1:235113908:CAC:C	acceptor_gain	1.0000
1:235113909:ACC:A	acceptor_loss	1.0000
1:235113910:CCTG:C	acceptor_loss	1.0000
1:235113911:C:A	acceptor_loss	1.0000
1:235113912:T:A	acceptor_loss	1.0000
1:235119815:TACCT:T	donor_loss	1.0000
1:235119817:CCTT:C	donor_loss	1.0000
1:235119831:CTCT:C	donor_gain	1.0000
1:235119832:TCTT:T	donor_gain	1.0000
1:235119833:CTTC:C	donor_gain	1.0000
1:235119895:GGTAA:G	acceptor_gain	1.0000
1:235119896:GTAA:G	acceptor_gain	1.0000
1:235119897:TAA:T	acceptor_gain	1.0000
1:235119898:AA:A	acceptor_gain	1.0000
1:235119900:C:CC	acceptor_gain	1.0000
1:235119906:A:AC	acceptor_gain	1.0000
1:235122322:TTA:T	donor_loss	1.0000
1:235122323:TACCT:T	donor_loss	1.0000
1:235122325:C:G	donor_loss	1.0000
1:235122369:CTTC:C	acceptor_gain	1.0000
1:235122373:C:A	acceptor_loss	1.0000
1:235122373:C:CC	acceptor_gain	1.0000
1:235122374:T:A	acceptor_loss	1.0000
1:235128593:A:AC	donor_gain	1.0000

AlphaMissense

943 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:235113793:A:G	L123P	1.000
1:235113796:A:G	L122P	1.000
1:235113796:A:T	L122H	1.000
1:235113804:G:C	F119L	1.000
1:235113804:G:T	F119L	1.000
1:235113806:A:G	F119L	1.000
1:235113820:A:G	L114P	1.000
1:235113820:A:T	L114H	1.000
1:235113832:A:G	L110S	1.000
1:235113841:A:G	L107P	1.000
1:235113844:A:G	L106S	1.000
1:235113863:A:G	C100R	1.000
1:235113865:A:T	V99E	1.000
1:235113868:G:T	A98D	1.000
1:235113869:C:G	A98P	1.000
1:235113871:A:T	I97N	1.000
1:235113874:G:A	A96V	1.000
1:235113874:G:T	A96E	1.000
1:235113875:C:G	A96P	1.000
1:235113883:A:G	L93P	1.000
1:235113883:A:T	L93Q	1.000
1:235113895:C:T	G89D	1.000
1:235113896:C:G	G89R	1.000
1:235119826:A:G	L81P	1.000
1:235119835:T:A	E78V	1.000
1:235119838:C:A	G77V	1.000
1:235119838:C:T	G77D	1.000
1:235119839:C:A	G77C	1.000
1:235119839:C:G	G77R	1.000
1:235119839:C:T	G77S	1.000

dbSNP variants (sampled 300 via entrez): RS1000069858 (1:235114263 G>A), RS1000313535 (1:235129271 A>G), RS1000563106 (1:235117968 C>A), RS1000618978 (1:235123434 G>C), RS1000625408 (1:235112264 C>A,T), RS1000627550 (1:235123986 T>A), RS1000658723 (1:235123641 A>G), RS1001087201 (1:235117828 C>T), RS1001155409 (1:235114564 C>G,T), RS1001186174 (1:235117716 T>C), RS1001206409 (1:235114897 T>C), RS1001368501 (1:235118717 G>A), RS1001435449 (1:235117517 A>G), RS1001506239 (1:235124240 G>A), RS1001820425 (1:235129568 C>T)

Disease associations

OMIM: gene MIM:601848 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST000759_2	LDL cholesterol	9.000000e-12
GCST000760_1	Cholesterol, total	5.000000e-14
GCST001535_14	Immune reponse to smallpox (secreted IL-2)	5.000000e-10
GCST001762_91	Obesity-related traits	7.000000e-06
GCST002930_11	Cobalt levels	4.000000e-06
GCST003542_147	Night sleep phenotypes	8.000000e-07
GCST010241_279	Apolipoprotein A1 levels	5.000000e-09
GCST010245_74	LDL cholesterol levels	2.000000e-10
GCST90011900_35	Serum alkaline phosphatase levels	3.000000e-14

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004574	total cholesterol measurement
EFO:0004645	response to vaccine
EFO:0004873	cytokine measurement
EFO:0005189	respiratory quotient
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Doxorubicin	increases expression, decreases response to substance, decreases expression, decreases reaction	3
Valproic Acid	increases expression, affects expression, decreases expression, affects cotreatment	3
Cadmium Chloride	increases expression, decreases expression, increases abundance	3
bisphenol A	affects expression, decreases expression, increases methylation	2
bisphenol S	affects cotreatment, decreases methylation, increases expression	2
Cadmium	increases expression, decreases expression, increases abundance	2
Diethylhexyl Phthalate	affects cotreatment, increases degradation, decreases expression	2
Paraquat	affects reaction, decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Cyclosporine	affects cotreatment, increases expression, decreases expression, decreases reaction	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
uranyl acetate	affects expression	1
1,12-benzoperylene	affects localization	1
deoxynivalenol	affects localization, increases phosphorylation	1
di-n-octyl phthalate	decreases expression	1
mono-(2-ethylhexyl)phthalate	affects cotreatment, decreases reaction, increases degradation, increases reaction	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
3-methyladenine	decreases expression, decreases reaction	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	affects cotreatment, increases expression	1
gossypol acetic acid	affects reaction, decreases expression	1
aflatoxin B2	decreases methylation	1
pepstatin	decreases expression, decreases reaction	1
dimethoxyethyl phthalate	affects expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
lactacystin	affects localization	1
chloropicrin	increases expression	1

Cellosaurus cell lines

9 cell lines: 9 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_F1KX	HT809-TH-tdTomato-LysoIP-MitoIP	Induced pluripotent stem cell	Male
CVCL_F1KY	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 KO/KO	Induced pluripotent stem cell	Male
CVCL_F1KZ	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 WT/WT	Induced pluripotent stem cell	Male
CVCL_F1L0	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 WT/L444P	Induced pluripotent stem cell	Male
CVCL_F1L1	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 L444P/L444P	Induced pluripotent stem cell	Male
CVCL_F1L2	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 KO/KO + GPNMB KO	Induced pluripotent stem cell	Male
CVCL_F1L3	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 WT/WT + GPNMB KO	Induced pluripotent stem cell	Male
CVCL_F1L4	HT809-TH-tdTomato-LysoIP-MitoIP-GBA1 L444P/L444P + GPNMB KO	Induced pluripotent stem cell	Male
CVCL_F1L5	HT809-TH-tdTomato-LysoIP-MitoIP + GPNMB KO	Induced pluripotent stem cell	Male

Clinical trials (associated diseases)

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