TPD52L1

gene
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Also known as D53hD53TPD53

Summary

TPD52L1 (TPD52 like 1, HGNC:12006) is a protein-coding gene on chromosome 6q22.31, encoding Tumor protein D53 (Q16890).

This gene encodes a member of a family of proteins that contain coiled-coil domains and may form hetero- or homomers. The encoded protein is involved in cell proliferation and calcium signaling. It also interacts with the mitogen-activated protein kinase kinase kinase 5 (MAP3K5/ASK1) and positively regulates MAP3K5-induced apoptosis. Multiple alternatively spliced transcript variants have been observed.

Source: NCBI Gene 7164 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 36 total
  • MANE Select transcript: NM_003287

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12006
Approved symbolTPD52L1
NameTPD52 like 1
Location6q22.31
Locus typegene with protein product
StatusApproved
AliasesD53, hD53, TPD53
Ensembl geneENSG00000111907
Ensembl biotypeprotein_coding
OMIM604069
Entrez7164

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000304877, ENST00000368388, ENST00000368402, ENST00000392482, ENST00000392483, ENST00000524679, ENST00000527711, ENST00000528193, ENST00000530868, ENST00000532423, ENST00000532429, ENST00000532978, ENST00000534000, ENST00000534199, ENST00000534368, ENST00000571678, ENST00000576089

RefSeq mRNA: 8 — MANE Select: NM_003287 NM_001003395, NM_001003396, NM_001003397, NM_001292026, NM_001300994, NM_001318903, NM_001318907, NM_003287

CCDS: CCDS34527, CCDS34528, CCDS43502, CCDS5130, CCDS75513, CCDS75514, CCDS83122

Canonical transcript exons

ENST00000534000 — 7 exons

ExonStartEnd
ENSE00002194959125153773125153970
ENSE00003508867125248282125248383
ENSE00003600857125229118125229266
ENSE00003617631125253717125253755
ENSE00003675275125257098125257158
ENSE00003687765125220078125220193
ENSE00003692658125262834125264407

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 99.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 45.7837 / max 1387.3505, expressed in 1407 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
6964423.78061219
6964312.48201264
696457.3007805
696470.5730347
696480.5490130
696460.4536181
696560.236856
696570.144021
696540.128521
696530.059716

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183199.83gold quality
right adrenal gland cortexUBERON:003582799.40gold quality
germinal epithelium of ovaryUBERON:000130499.36gold quality
right adrenal glandUBERON:000123399.34gold quality
adrenal cortexUBERON:000123599.17gold quality
left adrenal glandUBERON:000123499.16gold quality
left adrenal gland cortexUBERON:003582599.13gold quality
cervix squamous epitheliumUBERON:000692299.08gold quality
putamenUBERON:000187498.87gold quality
choroid plexus epitheliumUBERON:000391198.80gold quality
pancreatic ductal cellCL:000207998.78gold quality
saliva-secreting glandUBERON:000104498.69gold quality
minor salivary glandUBERON:000183098.57gold quality
tongue squamous epitheliumUBERON:000691998.56gold quality
mouth mucosaUBERON:000372998.53gold quality
squamous epitheliumUBERON:000691498.45gold quality
esophagus squamous epitheliumUBERON:000692098.40gold quality
lateral globus pallidusUBERON:000247698.39gold quality
nucleus accumbensUBERON:000188298.38gold quality
gingival epitheliumUBERON:000194998.34gold quality
esophagus mucosaUBERON:000246998.33gold quality
gingivaUBERON:000182898.22gold quality
caudate nucleusUBERON:000187398.22gold quality
gluteal muscleUBERON:000200097.93gold quality
epithelium of esophagusUBERON:000197697.91gold quality
triceps brachiiUBERON:000150997.88gold quality
lower esophagus mucosaUBERON:003583497.81gold quality
adrenal glandUBERON:000236997.79gold quality
penisUBERON:000098997.78gold quality
pharyngeal mucosaUBERON:000035597.74gold quality

Single-cell (SCXA)

Detected in 14 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-GEOD-180759yes1576.02
E-GEOD-98556yes560.56
E-HCAD-1yes241.81
E-HCAD-35yes80.49
E-GEOD-135922yes47.52
E-MTAB-10287yes47.27
E-HCAD-10yes22.55
E-GEOD-84465yes12.70
E-MTAB-7249yes11.29
E-MTAB-10137yes8.68
E-HCAD-30no880.00
E-ENAD-21no420.76
E-GEOD-124858no236.18
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

65 targeting TPD52L1, 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-5011-5P100.0083.465820
HSA-MIR-3924100.0072.092394
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-126-5P100.0072.713180
HSA-MIR-453199.9969.703181
HSA-MIR-539-3P99.9870.741616
HSA-MIR-485-3P99.9870.681585
HSA-MIR-548P99.9872.253784
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-365899.9673.874379
HSA-MIR-335-3P99.9373.364958
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-368699.9070.532432
HSA-MIR-430299.8967.941187
HSA-MIR-806299.8868.43995
HSA-MIR-4671-3P99.8872.461045
HSA-MIR-449299.8768.253611
HSA-MIR-469899.8471.414303
HSA-MIR-57799.7869.132479
HSA-MIR-471999.7372.103329
HSA-MIR-430699.7270.503630
HSA-MIR-4524A-3P99.7266.852406

Literature-anchored findings (GeneRIF, showing 3)

  • These results identify 14-3-3 proteins as partners for hD53, and alternative splicing as a mechanism for regulating 14-3-3 binding. (PMID:12963375)
  • a member of the tumor protein D52 family involved in cell proliferation and calcium signaling, up-regulates the ASK1-induced apoptosis [D53L1] (PMID:14761963)
  • The results indicate that tumor protein D52-like 1 genes are not ubiquitously expressed in leukemic bone marrow in children, and that RNA sample parameters may influence measures of gene expression more than commonly appreciated. (PMID:16620967)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotpd52l1ENSDARG00000042548
mus_musculusTpd52l1ENSMUSG00000000296
rattus_norvegicusTpd52l1ENSRNOG00000021478
drosophila_melanogasterCG5174FBGN0034345
caenorhabditis_elegansWBGENE00008745

Paralogs (3): TPD52 (ENSG00000076554), TPD52L2 (ENSG00000101150), TPD52L3 (ENSG00000170777)

Protein

Protein identifiers

Tumor protein D53Q16890 (reviewed: Q16890)

Alternative names: Tumor protein D52-like 1

All UniProt accessions (5): Q16890, E9PNK6, E9PNQ9, E9PPQ1, J3KNE7

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Forms a homodimer or heterodimer with other members of the family.

Similarity. Belongs to the TPD52 family.

Isoforms (5)

UniProt IDNamesCanonical?
Q16890-11yes
Q16890-22
Q16890-33
Q16890-44, +5hD53
Q16890-55

RefSeq proteins (8): NP_001003395, NP_001003396, NP_001003397, NP_001278955, NP_001287923, NP_001305832, NP_001305836, NP_003278* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007327TPD52Family

Pfam: PF04201

UniProt features (19 total): modified residue 8, splice variant 5, sequence conflict 2, chain 1, region of interest 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16890-F165.600.16

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 (8): 174, 29, 86, 122, 131, 133, 146, 149

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-432722Golgi Associated Vesicle Biogenesis

MSigDB gene sets: 216 (showing top): GOBP_REGULATION_OF_PHOSPHORYLATION, JAEGER_METASTASIS_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, REACTOME_MEMBRANE_TRAFFICKING, MORF_RAD51L3, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, GOBP_APOPTOTIC_SIGNALING_PATHWAY

GO Biological Process (4): G2/M transition of mitotic cell cycle (GO:0000086), positive regulation of MAP kinase activity (GO:0043406), positive regulation of JNK cascade (GO:0046330), positive regulation of apoptotic signaling pathway (GO:2001235)

GO Molecular Function (3): identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), protein binding (GO:0005515)

GO Cellular Component (2): cytoplasm (GO:0005737), perinuclear region of cytoplasm (GO:0048471)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
trans-Golgi Network Vesicle Budding1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
positive regulation of MAPK cascade2
cellular anatomical structure2
mitotic cell cycle1
mitotic cell cycle phase transition1
cell cycle G2/M phase transition1
MAP kinase activity1
regulation of MAP kinase activity1
positive regulation of protein serine/threonine kinase activity1
JNK cascade1
regulation of JNK cascade1
positive regulation of signal transduction1
positive regulation of apoptotic process1
apoptotic signaling pathway1
regulation of apoptotic signaling pathway1
protein binding1
identical protein binding1
protein dimerization activity1
binding1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

660 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TPD52L1KDELR2P33947572
TPD52L1LRIG3Q6UXM1567
TPD52L1SLC34A2O95436511
TPD52L1TMEM106BQ9NUM4506
TPD52L1TPD52L2O43399498
TPD52L1RETP07949481
TPD52L1GOPCQ9HD26448
TPD52L1LIMA1Q9UHB6447
TPD52L1RRP8O43159414
TPD52L1SLC6A17Q9H1V8393
TPD52L1FAM135BQ49AJ0380
TPD52L1BBXQ8WY36374
TPD52L1ROS1P08922371
TPD52L1TPM3P06753370
TPD52L1SDC4P31431370

IntAct

56 interactions, top by confidence:

ABTypeScore
PSMC3PSMD9psi-mi:“MI:0914”(association)0.940
YWHABTPD52L1psi-mi:“MI:0407”(direct interaction)0.690
YWHABTPD52L1psi-mi:“MI:0915”(physical association)0.690
TPD52TPD52L1psi-mi:“MI:0915”(physical association)0.660
TPD52L1TPD52psi-mi:“MI:0915”(physical association)0.660
YWHAGBLTP3Bpsi-mi:“MI:0914”(association)0.640
PSMC3PSMD12psi-mi:“MI:0914”(association)0.640
YWHABBLTP3Bpsi-mi:“MI:0914”(association)0.610
YWHAZTPD52L1psi-mi:“MI:0407”(direct interaction)0.590
YWHAZTPD52L1psi-mi:“MI:0915”(physical association)0.590
YWHAHBLTP3Bpsi-mi:“MI:0914”(association)0.570
TPD52L3TPD52L2psi-mi:“MI:0914”(association)0.530
TPD52L1TPD52L2psi-mi:“MI:0914”(association)0.530
AZIN2OAZ2psi-mi:“MI:0914”(association)0.530
TPD52TPD52L2psi-mi:“MI:0914”(association)0.530
AGMATDCXpsi-mi:“MI:0914”(association)0.500
TPD52L1DAPK1psi-mi:“MI:0407”(direct interaction)0.440
ABL2TPD52L1psi-mi:“MI:0915”(physical association)0.370
TPD52L1PAK6psi-mi:“MI:0915”(physical association)0.370
SFNTPD52L1psi-mi:“MI:0915”(physical association)0.370
Tpd52TPD52L1psi-mi:“MI:0915”(physical association)0.370

BioGRID (57): TPD52L1 (Affinity Capture-MS), ISYNA1 (Co-fractionation), TPD52L1 (Co-fractionation), TPD52L1 (Co-fractionation), UCHL3 (Co-fractionation), TPD52L1 (Affinity Capture-MS), TPD52L1 (Affinity Capture-MS), TPD52L1 (Affinity Capture-MS), TPD52L1 (Affinity Capture-RNA), TPD52L1 (Reconstituted Complex), TPD52L1 (Two-hybrid), GPR135 (Two-hybrid), HDAC1 (Two-hybrid), YAE1D1 (Two-hybrid), EIF3J (Two-hybrid)

ESM2 similar proteins: A5D7H2, A6QPI6, E1BWM5, F1N5S9, F1QH17, O35094, O43399, O43615, O54818, O60941, O70585, P55327, P58405, P84060, Q13033, Q16890, Q4R3C7, Q5BJS4, Q5R812, Q5RCT1, Q5SRX1, Q5VWJ9, Q5XGW6, Q5ZHP5, Q5ZJB7, Q5ZMQ0, Q62393, Q6GL11, Q6PCT3, Q6ZVM7, Q75Q41, Q8CE50, Q8IVP5, Q8K1Z0, Q8WUX9, Q95212, Q96IK1, Q96RU3, Q9CPQ3, Q9CYZ2

Diamond homologs: O43399, O54818, P55326, P55327, Q16890, Q5RCT1, Q62393, Q6PCT3, Q95212, Q96J77, Q9CYZ2, Q9I8F4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 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:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria6138.4×3e-10
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex6122.1×4e-10
SARS-CoV-1 targets host intracellular signalling and regulatory pathways6122.1×4e-10
Activation of BH3-only proteins690.3×2e-09
RHO GTPases activate PKNs767.3×4e-10
Intrinsic Pathway for Apoptosis653.2×4e-08
FOXO-mediated transcription550.9×1e-06
G2/M Checkpoints832.6×4e-09

GO biological processes:

GO termPartnersFoldFDR
intracellular protein localization616.1×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance22
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1579 predictions. Top by Δscore:

VariantEffectΔscore
6:125220064:A:AGacceptor_gain1.0000
6:125220069:T:Aacceptor_gain1.0000
6:125220167:G:GTdonor_gain1.0000
6:125220190:TCAG:Tdonor_loss1.0000
6:125220191:CAGGT:Cdonor_loss1.0000
6:125220193:GGTA:Gdonor_loss1.0000
6:125220194:G:Cdonor_loss1.0000
6:125220195:T:Gdonor_loss1.0000
6:125229108:C:CAacceptor_gain1.0000
6:125229114:GTA:Gacceptor_loss1.0000
6:125229115:TAGC:Tacceptor_loss1.0000
6:125229116:A:AGacceptor_gain1.0000
6:125229116:A:Gacceptor_loss1.0000
6:125229117:G:GAacceptor_gain1.0000
6:125229117:G:Tacceptor_loss1.0000
6:125229117:GCTA:Gacceptor_gain1.0000
6:125229262:ACTGC:Adonor_gain1.0000
6:125229263:CTGC:Cdonor_gain1.0000
6:125229264:TGC:Tdonor_gain1.0000
6:125229265:GC:Gdonor_gain1.0000
6:125229265:GCG:Gdonor_gain1.0000
6:125229266:CGT:Cdonor_loss1.0000
6:125229267:G:GGdonor_gain1.0000
6:125229267:G:Tdonor_loss1.0000
6:125229268:TA:Tdonor_loss1.0000
6:125229269:AA:Adonor_loss1.0000
6:125248280:A:AGacceptor_gain1.0000
6:125248281:G:GAacceptor_gain1.0000
6:125248281:GC:Gacceptor_gain1.0000
6:125248281:GCTA:Gacceptor_gain1.0000

AlphaMissense

1358 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:125248347:T:AV117D0.997
6:125229161:A:TK60I0.995
6:125248335:C:AA113D0.995
6:125248325:G:CA110P0.994
6:125248313:G:CA106P0.993
6:125229140:T:CL53P0.992
6:125229162:A:CK60N0.992
6:125229162:A:TK60N0.992
6:125248359:T:AI121N0.992
6:125257133:T:AV154D0.991
6:125257145:T:AV158D0.991
6:125248283:T:GY96D0.990
6:125248314:C:AA106E0.988
6:125257111:T:CF147L0.986
6:125257113:C:AF147L0.986
6:125257113:C:GF147L0.986
6:125248334:G:CA113P0.985
6:125229119:T:CL46P0.984
6:125229143:G:CR54P0.984
6:125229173:T:CL64P0.983
6:125229241:T:AW87R0.983
6:125229241:T:CW87R0.983
6:125248359:T:GI121S0.983
6:125257098:G:CR142S0.983
6:125257098:G:TR142S0.983
6:125229157:G:CA59P0.982
6:125248326:C:AA110E0.982
6:125257112:T:CF147S0.981
6:125257121:T:CF150S0.981
6:125248355:G:CA120P0.977

dbSNP variants (sampled 300 via entrez): RS1000027106 (6:125230362 G>T), RS1000084038 (6:125229782 G>T), RS1000090963 (6:125224016 G>T), RS1000118764 (6:125222688 T>C), RS1000142717 (6:125180579 C>T), RS1000161050 (6:125206413 A>G), RS1000210680 (6:125155678 A>T), RS1000234134 (6:125164076 G>A), RS1000277374 (6:125249263 T>C), RS1000315547 (6:125235791 A>T), RS1000346003 (6:125200199 G>A), RS1000366031 (6:125152626 G>T), RS1000392768 (6:125243102 T>C), RS1000445352 (6:125158411 T>C,G), RS1000474960 (6:125158514 T>A,C)

Disease associations

OMIM: gene MIM:604069 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003542_126Night sleep phenotypes9.000000e-06
GCST012489_109Heel bone mineral density x serum urate levels interaction2.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004531urate measurement
EFO:0009270heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Estradiolaffects expression, affects cotreatment, increases expression, decreases expression8
Valproic Acidaffects expression, affects cotreatment, increases expression7
trichostatin Aaffects cotreatment, increases expression3
Cyclosporinedecreases expression, increases expression3
Cadmium Chlorideincreases expression, decreases expression3
mercuric bromideincreases expression, affects cotreatment2
entinostatincreases expression, affects cotreatment2
belinostatincreases expression, affects cotreatment2
Zoledronic Aciddecreases expression2
Vorinostataffects cotreatment, increases expression2
Panobinostataffects cotreatment, increases expression2
Acetaminophendecreases expression, increases expression2
Calcitriolincreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Progesteroneincreases expression, decreases expression, affects cotreatment2
Testosteroneaffects cotreatment, increases expression2
Tretinoinincreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
testosterone enanthateaffects expression1
daidzeinincreases expression1
methylmercuric chlorideincreases expression1
bisphenol Adecreases expression1
glycidyl methacrylatedecreases expression1
ferric ammonium citrateincreases expression, decreases reaction1
beta-lapachonedecreases expression1
afimoxifenedecreases reaction, increases expression1
sodium arseniteincreases expression1
perfluorooctanoic acidincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
N-acetyl-4-benzoquinoneimineaffects response to substance1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2JEAbcam HeLa TPD52L1 KOCancer cell lineFemale

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.