TECPR1

gene
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Also known as DKFZP434B0335FLJ23419FLJ90593KIAA1358

Summary

TECPR1 (tectonin beta-propeller repeat containing 1, HGNC:22214) is a protein-coding gene on chromosome 7q21.3, encoding Tectonin beta-propeller repeat-containing protein 1 (Q7Z6L1). Tethering factor involved in autophagy.

This gene encodes a tethering factor involved in autophagy. The encoded protein is found at autolysosomes, and is involved in targeting protein aggregates, damaged mitochondria, and bacterial pathogens for autophagy

Source: NCBI Gene 25851 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 246 total — 2 likely-pathogenic
  • MANE Select transcript: NM_015395

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:22214
Approved symbolTECPR1
Nametectonin beta-propeller repeat containing 1
Location7q21.3
Locus typegene with protein product
StatusApproved
AliasesDKFZP434B0335, FLJ23419, FLJ90593, KIAA1358
Ensembl geneENSG00000205356
Ensembl biotypeprotein_coding
OMIM614781
Entrez25851

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 14 protein_coding, 7 retained_intron, 6 protein_coding_CDS_not_defined

ENST00000415086, ENST00000420697, ENST00000423128, ENST00000447648, ENST00000462511, ENST00000463402, ENST00000463648, ENST00000471397, ENST00000472845, ENST00000474915, ENST00000476659, ENST00000479911, ENST00000479975, ENST00000483740, ENST00000485716, ENST00000488667, ENST00000490842, ENST00000871694, ENST00000871695, ENST00000871696, ENST00000871697, ENST00000962624, ENST00000962625, ENST00000962626, ENST00000962627, ENST00000962628, ENST00000962629

RefSeq mRNA: 1 — MANE Select: NM_015395 NM_015395

CCDS: CCDS47648

Canonical transcript exons

ENST00000447648 — 26 exons

ExonStartEnd
ENSE000014825279823282798232972
ENSE000014825309823342198233911
ENSE000014825319823677698236921
ENSE000014825339823850998238610
ENSE000014825379824346798243592
ENSE000014825409824592298246165
ENSE000014825429825139498251548
ENSE000019155729825212698252232
ENSE000019249429821462498217503
ENSE000034727499822299098223170
ENSE000034744789823096198231118
ENSE000034763199824457198244693
ENSE000034918099822166198221753
ENSE000035017349822500698225102
ENSE000035088999823180498231959
ENSE000035108959822366298223718
ENSE000035218009824085198240951
ENSE000035248079822903998229166
ENSE000035338069823122498231373
ENSE000035734509821793698218042
ENSE000036075379821769298217811
ENSE000036090379824107098241244
ENSE000036155249822801498228116
ENSE000036264439824488598245067
ENSE000036286359822238698222521
ENSE000036422369822480198224880

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 99.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.2129 / max 77.1087, expressed in 1767 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
850438.21291767

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183199.22gold quality
pancreatic ductal cellCL:000207997.84gold quality
ileal mucosaUBERON:000033196.49gold quality
endothelial cellCL:000011594.37gold quality
sural nerveUBERON:001548893.89gold quality
tracheaUBERON:000312693.12gold quality
granulocyteCL:000009493.07gold quality
middle temporal gyrusUBERON:000277192.73gold quality
prefrontal cortexUBERON:000045192.39gold quality
tibialis anteriorUBERON:000138592.24gold quality
apex of heartUBERON:000209891.32gold quality
bloodUBERON:000017891.31gold quality
vermiform appendixUBERON:000115491.15gold quality
cortical plateUBERON:000534391.07gold quality
Brodmann (1909) area 23UBERON:001355490.65gold quality
frontal cortexUBERON:000187090.31gold quality
bone marrow cellCL:000209289.92gold quality
pituitary glandUBERON:000000789.72gold quality
cardiac muscle of right atriumUBERON:000337989.47silver quality
neocortexUBERON:000195089.42gold quality
nasal cavity epitheliumUBERON:000538489.26silver quality
caecumUBERON:000115389.08gold quality
entorhinal cortexUBERON:000272888.89gold quality
superior frontal gyrusUBERON:000266188.79gold quality
right frontal lobeUBERON:000281088.69gold quality
ganglionic eminenceUBERON:000402388.41gold quality
parietal lobeUBERON:000187288.28gold quality
upper arm skinUBERON:000426388.28silver quality
postcentral gyrusUBERON:000258188.21gold quality
right hemisphere of cerebellumUBERON:001489088.20gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes19.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting TECPR1, 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-5196-5P100.0067.982761
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-150-5P99.9966.691976
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-120899.7068.281533
HSA-MIR-320299.6667.702737
HSA-MIR-6715B-5P99.6469.631420
HSA-MIR-613299.6065.831554
HSA-MIR-6836-5P99.6065.621538
HSA-MIR-426999.5569.891373
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-203A-3P99.4970.562806
HSA-MIR-766-3P99.4765.241811
HSA-MIR-365A-3P99.4370.02836
HSA-MIR-365B-3P99.4370.02836
HSA-MIR-425199.4069.193363
HSA-MIR-128-1-5P99.3360.46332
HSA-MIR-128-2-5P99.3360.83311
HSA-MIR-3606-5P99.3169.671168
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-4685-5P99.2565.991563
HSA-MIR-6837-5P99.2565.471632
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-6761-5P98.7168.031504
HSA-MIR-374B-3P98.6368.241360

Literature-anchored findings (GeneRIF, showing 4)

  • The concerted interactions among TECPR1, Atg12-Atg5, and PtdIns(3)P provide the fusion specificity between autophagosomes and lysosomes and that the assembly of this complex initiates the autophagosome maturation process. (PMID:22342342)
  • TECPR1 promotes aggrephagy by direct recruitment of LC3C autophagosomes to lysosomes. (PMID:32532970)
  • TECPR1 Induces Apoptosis in Non-Small Cell Lung Carcinoma via ATG5 Upregulation-Induced Autophagy Promotion. (PMID:36197771)
  • TECPR1 is activated by damage-induced sphingomyelin exposure to mediate noncanonical autophagy. (PMID:37409525)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotecpr1aENSDARG00000062515
danio_reriotecpr1bENSDARG00000074086
mus_musculusTecpr1ENSMUSG00000066621
rattus_norvegicusTecpr1ENSRNOG00000001010
drosophila_melanogasterPex23FBGN0288469

Protein

Protein identifiers

Tectonin beta-propeller repeat-containing protein 1Q7Z6L1 (reviewed: Q7Z6L1)

All UniProt accessions (4): C9J2A1, C9JEV4, C9JUV4, Q7Z6L1

UniProt curated annotations — full annotation on UniProt →

Function. Tethering factor involved in autophagy. Involved in autophagosome maturation by promoting the autophagosome fusion with lysosomes: acts by associating with both the ATG5-ATG12 conjugate and phosphatidylinositol-3-phosphate (PtdIns(3)P) present at the surface of autophagosomes. Also involved in selective autophagy against bacterial pathogens, by being required for phagophore/preautophagosomal structure biogenesis and maturation.

Subunit / interactions. Interacts with ATG5; the interaction is direct. Interacts with WIPI2. Interacts with the ATG5-ATG12 conjugate, the interaction is however mutually exclusive with ATG16, since it does not interact with ATG12-ATG5-ATG16 complex.

Subcellular location. Cytoplasmic vesicle. Autophagosome membrane. Lysosome membrane.

Domain organisation. The PH domain mediates the binding to phosphatidylinositol-3-phosphate (PtdIns(3)P). While full-length protein is unable to bind PtdIns(3)P in vitro, it is assumed that the binding to the ATG5-ATG12 conjugate exposes the PH domain, allowing the association with PtdIns(3)P.

Similarity. Belongs to the TECPR1 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q7Z6L1-11yes
Q7Z6L1-22
Q7Z6L1-33
Q7Z6L1-44

RefSeq proteins (1): NP_056210* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006614Peroxin/FerlinDomain
IPR006624Beta-propeller_rpt_TECPRRepeat
IPR010482TECPR1-like_DysFDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR051513Tectonin_beta-propFamily

Pfam: PF06398, PF06462, PF19193

UniProt features (38 total): repeat 9, modified residue 7, splice variant 6, sequence conflict 6, region of interest 2, sequence variant 2, chain 1, compositionally biased region 1, helix 1, turn 1, strand 1, domain 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
4TQ1X-RAY DIFFRACTION1.8
8P5PX-RAY DIFFRACTION1.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z6L1-F179.530.48

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 (7): 386, 388, 391, 412, 417, 938, 949

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GOBP_REGULATION_OF_AUTOPHAGY, GOCC_VACUOLAR_MEMBRANE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MACROAUTOPHAGY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, HEN1_01, LIAO_METASTASIS, MYOD_Q6, NRF2_Q4, BROWN_MYELOID_CELL_DEVELOPMENT_UP, CUI_TCF21_TARGETS_2_DN, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, GOCC_AUTOPHAGOSOME, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN

GO Biological Process (4): autophagy (GO:0006914), macroautophagy (GO:0016236), autophagosome maturation (GO:0097352), regulation of autophagosome maturation (GO:1901096)

GO Molecular Function (3): phosphatidylinositol-3-phosphate binding (GO:0032266), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (9): autophagosome membrane (GO:0000421), nucleoplasm (GO:0005654), lysosomal membrane (GO:0005765), cytoplasmic vesicle (GO:0031410), protein-containing complex (GO:0032991), cytoplasm (GO:0005737), lysosome (GO:0005764), membrane (GO:0016020), bounding membrane of organelle (GO:0098588)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
binding2
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
autophagosome assembly1
autophagy1
macroautophagy1
protein-containing complex disassembly1
regulation of macroautophagy1
regulation of organelle organization1
regulation of protein-containing complex disassembly1
autophagosome maturation1
phosphatidylinositol phosphate binding1
vacuolar membrane1
autophagosome1
nuclear lumen1
lysosome1
lytic vacuole membrane1
cytoplasm1
intracellular vesicle1
cellular_component1
intracellular anatomical structure1
lytic vacuole1
organelle membrane1

Protein interactions and networks

STRING

1677 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TECPR1ATG5Q9H1Y0992
TECPR1ATG12O94817979
TECPR1WIPI2Q9Y4P8977
TECPR1WIPI1Q5MNZ9747
TECPR1ATG16L1Q676U5724
TECPR1PLEKHM1Q9Y4G2681
TECPR1GABARAPL2P60520654
TECPR1F5GZY7F5GZY7646
TECPR1ATG3Q9NT62641
TECPR1EPG5Q9HCE0589
TECPR1CALCOCO2Q13137466
TECPR1TRAPPC12Q8WVT3437
TECPR1STX17P56962434
TECPR1MAP1LC3CQ9BXW4433
TECPR1ATG14Q6ZNE5418

IntAct

30 interactions, top by confidence:

ABTypeScore
TECPR1ATG5psi-mi:“MI:0915”(physical association)0.820
ATG5ATG12psi-mi:“MI:0914”(association)0.800
CFTRESYT2psi-mi:“MI:0914”(association)0.710
ATG3MAP1LC3B2psi-mi:“MI:0914”(association)0.530
ATG3TECPR1psi-mi:“MI:0915”(physical association)0.500
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
TECPR1H1-2psi-mi:“MI:0915”(physical association)0.400
TECPR1PRPF8psi-mi:“MI:0915”(physical association)0.400
ATG5IGKV1-5psi-mi:“MI:0914”(association)0.350
FYCO1SEC24Bpsi-mi:“MI:0914”(association)0.350
TECPR1PLOD3psi-mi:“MI:0914”(association)0.350
ATG12GABARAPpsi-mi:“MI:0914”(association)0.350
ATG5PLOD2psi-mi:“MI:0914”(association)0.350
BECN1psi-mi:“MI:0914”(association)0.350
ATG12EMC8psi-mi:“MI:0914”(association)0.350
CDH5ESYT2psi-mi:“MI:2364”(proximity)0.270
STXBP1TECPR1psi-mi:“MI:0915”(physical association)0.000
ATG5TECPR1psi-mi:“MI:0915”(physical association)0.000

BioGRID (32): TECPR1 (Co-crystal Structure), TECPR1 (Two-hybrid), TECPR1 (Reconstituted Complex), TECPR1 (Two-hybrid), ATG5 (Reconstituted Complex), TECPR1 (Proximity Label-MS), TECPR1 (Proximity Label-MS), TECPR1 (Affinity Capture-RNA), TECPR1 (Affinity Capture-MS), TECPR1 (Affinity Capture-MS), TECPR1 (Affinity Capture-MS), TECPR1 (Protein-peptide), TMEM63B (Cross-Linking-MS (XL-MS)), TECPR1 (Affinity Capture-MS), TECPR1 (Affinity Capture-MS)

ESM2 similar proteins: A1L3L1, A2RT67, A2RUS2, A3KPW7, A4IJ06, A6QNT4, D2HNY3, D3ZV31, E1BGQ2, E1C3P4, F1R7R1, O15040, O75031, P48553, P50747, Q0IHB3, Q2TBA3, Q3TLI0, Q3U0J8, Q3ZBA0, Q3ZBK7, Q496Y0, Q5F3F2, Q5M7Q1, Q5R5Y0, Q5ZJK1, Q66H91, Q69ZK0, Q69ZT1, Q6GR37, Q6NTL4, Q6VNB8, Q7TPQ3, Q7Z6L1, Q80VP0, Q8BKW4, Q8BXK4, Q8HXH0, Q8IWR0, Q8IYL2

Diamond homologs: A9JRJ2, E1BZR9, O94611, Q3ZBA0, Q5R5Y0, Q7Z6L1, Q80VP0, Q9VWB0, O44126, P36573, Q09581, Q9JL15

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 19 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
Macroautophagy538.5×1e-05

GO biological processes:

GO termPartnersFoldFDR
autophagosome assembly674.9×3e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic2
Uncertain significance192
Likely benign7
Benign4

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
916572NM_015395.3(TECPR1):c.2617G>A (p.Asp873Asn)Likely pathogenic
982232NM_015395.3(TECPR1):c.2899C>T (p.Arg967Cys)Likely pathogenic

SpliceAI

4810 predictions. Top by Δscore:

VariantEffectΔscore
7:98217920:C:CAdonor_gain1.0000
7:98222379:CACT:Cdonor_loss1.0000
7:98222380:ACTC:Adonor_loss1.0000
7:98222381:CT:Cdonor_loss1.0000
7:98222382:TCA:Tdonor_loss1.0000
7:98222383:CAC:Cdonor_loss1.0000
7:98222384:A:ACdonor_gain1.0000
7:98222384:A:Cdonor_loss1.0000
7:98222385:C:CCdonor_gain1.0000
7:98222385:CCGG:Cdonor_gain1.0000
7:98222517:GAGCC:Gacceptor_gain1.0000
7:98222519:GCC:Gacceptor_gain1.0000
7:98222520:CC:Cacceptor_gain1.0000
7:98222520:CCC:Cacceptor_gain1.0000
7:98222521:CC:Cacceptor_gain1.0000
7:98222522:C:CCacceptor_gain1.0000
7:98222522:C:Tacceptor_gain1.0000
7:98222983:CACT:Cdonor_loss1.0000
7:98222984:ACTC:Adonor_loss1.0000
7:98222985:CTCA:Cdonor_loss1.0000
7:98222986:TCA:Tdonor_loss1.0000
7:98222987:CACCG:Cdonor_loss1.0000
7:98222988:A:ACdonor_gain1.0000
7:98222989:C:CCdonor_gain1.0000
7:98222989:C:CGdonor_loss1.0000
7:98222989:CCG:Cdonor_gain1.0000
7:98228009:CTTA:Cdonor_loss1.0000
7:98228010:TTAC:Tdonor_loss1.0000
7:98228011:TA:Tdonor_loss1.0000
7:98228013:C:CAdonor_loss1.0000

AlphaMissense

7619 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:98217989:A:GW1071R0.999
7:98217989:A:TW1071R0.999
7:98222512:A:GW980R0.999
7:98222512:A:TW980R0.999
7:98223679:C:AR910S0.999
7:98223679:C:GR910S0.999
7:98223680:C:GR910T0.999
7:98224826:A:GW889R0.999
7:98224826:A:TW889R0.999
7:98217709:A:GW1123R0.998
7:98217709:A:TW1123R0.998
7:98217987:C:AW1071C0.998
7:98217987:C:GW1071C0.998
7:98221745:A:GW1025R0.998
7:98221745:A:TW1025R0.998
7:98223142:A:GW926R0.998
7:98223142:A:TW926R0.998
7:98223676:C:AR911S0.998
7:98223676:C:GR911S0.998
7:98223680:C:AR910M0.998
7:98224824:C:AW889C0.998
7:98224824:C:GW889C0.998
7:98224871:A:GW874R0.998
7:98224871:A:TW874R0.998
7:98225077:A:GW847R0.998
7:98225077:A:TW847R0.998
7:98228042:A:GW829R0.998
7:98228042:A:TW829R0.998
7:98228045:G:TR828S0.998
7:98229105:A:GW782R0.998

dbSNP variants (sampled 300 via entrez): RS1000104157 (7:98245239 A>C), RS1000189366 (7:98242028 T>C), RS1000191248 (7:98230065 C>G), RS1000272864 (7:98245019 G>A), RS1000360363 (7:98215339 T>G), RS1000431052 (7:98253034 G>C), RS1000583312 (7:98247021 G>A,T), RS1000585491 (7:98219619 C>A,T), RS1000673098 (7:98234384 C>A,T), RS1000759598 (7:98253325 A>G), RS1000794856 (7:98240505 C>T), RS1000822954 (7:98233226 G>A), RS1000879074 (7:98217865 G>A), RS1000884980 (7:98229445 T>C), RS1000931003 (7:98234626 T>A)

Disease associations

OMIM: gene MIM:614781 | disease phenotypes: MIM:189960

GenCC curated gene-disease

Mondo (1): esophageal atresia/tracheoesophageal fistula (MONDO:0008586)

Orphanet (2): Esophageal atresia (Orphanet:1199), Moyamoya angiopathy (Orphanet:477768)

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008971_65Urate levels2.000000e-08
GCST008972_40Urate levels2.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004531urate measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C531835Esophageal atresia with or without tracheoesophageal fistula (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Adecreases methylation1
beta-lapachonedecreases expression1
sodium arseniteincreases expression1
aflatoxin B2decreases methylation1
sulphoraphenedecreases expression1
clothianidindecreases expression1
abrinedecreases expression1
Sunitinibincreases expression1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cisplatindecreases expression1
Doxorubicindecreases expression1
Ozoneaffects expression, increases abundance1
Smokedecreases expression1
Asbestos, Crocidolitedecreases expression1
Cadmium Chlorideincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03792360PHASE1WITHDRAWNAdipose Derived SVF for Aero-digestive & Enterocutaneous Fistulae
NCT02033772Not specifiedCOMPLETEDProspective Data Collection of Patients < 6 Months of Age Undergoing Thoracoscopic Surgery
NCT02364843Not specifiedTERMINATEDA Physiological Study to Determine the Enteral Threonine Requirements in Infants Aged 1 to 6 Months
NCT03455881Not specifiedUNKNOWNPhenotypic and Genetic Assessment of Tracheal and Esophageal Birth Defects in Patients
NCT03730454Not specifiedACTIVE_NOT_RECRUITINGTransanastomotic Tube for Proximal Esophageal Atresia With Distal Tracheoesophageal Fistula Repair