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ATG2A

gene
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Also known as KIAA0404BLTP4A

Summary

ATG2A (autophagy related 2A, HGNC:29028) is a protein-coding gene on chromosome 11q13.1, encoding Autophagy-related protein 2 homolog A (Q2TAZ0). Lipid transfer protein involved in autophagosome assembly.

Enables lipid transfer activity. Involved in autophagosome assembly and positive regulation of autophagosome assembly. Is active in organelle membrane contact site.

Source: NCBI Gene 23130 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 375 total
  • MANE Select transcript: NM_015104

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29028
Approved symbolATG2A
Nameautophagy related 2A
Location11q13.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0404, BLTP4A
Ensembl geneENSG00000110046
Ensembl biotypeprotein_coding
OMIM616225
Entrez23130

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 retained_intron

ENST00000377264, ENST00000418259, ENST00000461701, ENST00000472525, ENST00000879823, ENST00000879824, ENST00000879825, ENST00000879826, ENST00000934232, ENST00000934233

RefSeq mRNA: 3 — MANE Select: NM_015104 NM_001367971, NM_001367972, NM_015104

CCDS: CCDS31602

Canonical transcript exons

ENST00000377264 — 41 exons

ExonStartEnd
ENSE000007303346491408164914233
ENSE000007303366491382164913923
ENSE000007303816490574264905848
ENSE000008637436490088464901092
ENSE000008637446490196264902176
ENSE000008637456490251664902680
ENSE000008637506491303864913136
ENSE000010634676490968164909924
ENSE000011706826489529064895442
ENSE000011706896489646264896616
ENSE000011706996489674864896869
ENSE000011707106489741264897494
ENSE000011707216489767164897743
ENSE000011707296489783964897974
ENSE000011707376489808664898170
ENSE000011707466489826164898362
ENSE000011707576489863664898842
ENSE000011707676490049464900629
ENSE000011707956490226064902386
ENSE000011708126490328864903364
ENSE000011708246490359064903660
ENSE000011708326490556364905655
ENSE000011708486490611364906193
ENSE000011708576490633464906533
ENSE000011708646490666564906815
ENSE000011708736490725564907439
ENSE000011708816490752564907664
ENSE000011708876490774864907890
ENSE000011708946490899164909150
ENSE000011709036490927164909367
ENSE000011709216491004064910195
ENSE000011709286491061664910708
ENSE000011709366491080764910954
ENSE000011709426491103864911275
ENSE000011709496491184264911982
ENSE000011709576491208564912249
ENSE000011709656491232764912423
ENSE000011709776491326664913401
ENSE000016351096489454664895209
ENSE000018175836491696564917209
ENSE000037318426491433864914500

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 91.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.8353 / max 1604.0557, expressed in 1776 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
12050914.25341771
1205100.5819311

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111491.51gold quality
pancreatic ductal cellCL:000207990.42gold quality
bloodUBERON:000017890.30gold quality
skin of legUBERON:000151190.06gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451189.31gold quality
mucosa of stomachUBERON:000119989.19gold quality
skin of abdomenUBERON:000141689.12gold quality
granulocyteCL:000009488.98gold quality
zone of skinUBERON:000001488.30gold quality
left ovaryUBERON:000211987.89gold quality
adenohypophysisUBERON:000219687.71gold quality
liverUBERON:000210787.64gold quality
right hemisphere of cerebellumUBERON:001489087.57gold quality
mucosa of transverse colonUBERON:000499187.53gold quality
right ovaryUBERON:000211887.41gold quality
endometrium epitheliumUBERON:000481187.41gold quality
myocardiumUBERON:000234987.33silver quality
apex of heartUBERON:000209887.32gold quality
body of stomachUBERON:000116187.05gold quality
pituitary glandUBERON:000000786.96gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450286.88gold quality
endocervixUBERON:000045886.64gold quality
spleenUBERON:000210686.56gold quality
cerebellar hemisphereUBERON:000224586.48gold quality
cerebellar cortexUBERON:000212986.39gold quality
hindlimb stylopod muscleUBERON:000425286.37gold quality
right lungUBERON:000216786.34gold quality
ectocervixUBERON:001224986.29gold quality
metanephros cortexUBERON:001053386.26gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.13gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-4yes49.44
E-ANND-3yes5.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting ATG2A, 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-4481100.0066.421669
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-449299.8768.253611
HSA-MIR-629-3P99.8567.991875
HSA-MIR-449899.4767.422360
HSA-MIR-3614-5P99.3065.25837
HSA-MIR-1273H-3P99.2967.55980
HSA-MIR-450599.2767.812678
HSA-MIR-578799.2267.862628
HSA-MIR-7114-3P98.4266.53569
HSA-MIR-316698.2466.631223
HSA-MIR-1180-5P98.1665.32460
HSA-MIR-615-5P98.1063.76591
HSA-MIR-6842-3P98.0766.331325
HSA-MIR-466097.7967.441328
HSA-MIR-64797.7367.79927
HSA-MIR-27B-5P97.3466.55549
HSA-MIR-6773-5P97.0464.30595
HSA-MIR-874-5P96.9363.921014
HSA-MIR-6729-3P96.9166.79703
HSA-MIR-4436B-5P96.7168.371346
HSA-MIR-6724-5P96.4163.11507
HSA-MIR-541-3P96.0766.111271

Literature-anchored findings (GeneRIF, showing 13)

  • human hAtg2A can not function in autophagy in yeast, however, it is recruited to the preautophagosomal structure (PMID:21887408)
  • Depletion of both Atg2A and Atg2B causes clustering of enlarged lipid droplets in an autophagy-independent manner. These data suggest that mammalian Atg2 proteins function both in autophagosome formation and regulation of lipid droplet morphology and dispersion. (PMID:22219374)
  • These data provide evidence for additional roles of Atg2A and Atg14L in the formation of early autophagosomal membranes and also in lipid metabolism. (PMID:24776541)
  • Among polymorphisms identified in the present study, rs76974938 [C/T (D67N)] of C21orf59 and rs188780113 [G/A (R478C)] of ATG2A may be novel determinants of estimated glomerular filtration rate and chronic kidney disease or of the serum concentration of uric acid, respectively. (PMID:28410202)
  • Authors demonstrate that inhibition of autophagosome completion by Atg2A/B deletion accumulates immature autophagosomal membranes that promote non-canonical caspase-8 activation in response to nutrient starvation via an intracellular death-inducing signaling complex (iDISC). (PMID:28800131)
  • The N-terminal amino acids 1-198 and the C-terminal amino acids 1830-1938 are required for the localization to isolation membranes and lipid droplets, respectively. We also identified an amphipathic helix in ATG2A that is required for both its localization to organelles and autophagosome formation. (PMID:29113029)
  • N-terminal fragment of ATG2A that supports lipid transfer in vitro is both necessary and fully sufficient to rescue blocked autophagosome biogenesis in ATG2A/ATG2B KO cells (PMID:30952800)
  • Here, the authors demonstrate that human ATG2A is a lipid transfer protein. ATG2A can extract lipids from membrane vesicles and unload them to other vesicles. Lipid transfer by ATG2A is more efficient between tethered vesicles than between untethered vesicles. (PMID:31271352)
  • A conserved ATG2-GABARAP family interaction is critical for phagophore formation. (PMID:32009292)
  • HIF-1alpha-induced expression of m6A reader YTHDF1 drives hypoxia-induced autophagy and malignancy of hepatocellular carcinoma by promoting ATG2A and ATG14 translation. (PMID:33619246)
  • A model for a partnership of lipid transfer proteins and scramblases in membrane expansion and organelle biogenesis. (PMID:33850023)
  • Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation. (PMID:37115157)
  • MGCG regulates glioblastoma tumorigenicity via hnRNPK/ATG2A and promotes autophagy. (PMID:37460467)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioatg2aENSDARG00000101507
mus_musculusAtg2aENSMUSG00000024773
rattus_norvegicusAtg2aENSRNOG00000060707
drosophila_melanogasterAtg2FBGN0044452
caenorhabditis_elegansWBGENE00019748

Paralogs (1): ATG2B (ENSG00000066739)

Protein

Protein identifiers

Autophagy-related protein 2 homolog A — Q2TAZ0 (reviewed: Q2TAZ0)

All UniProt accessions (2): Q2TAZ0, H7C3T2

UniProt curated annotations — full annotation on UniProt →

Function. Lipid transfer protein involved in autophagosome assembly. Tethers the edge of the isolation membrane (IM) to the endoplasmic reticulum (ER) and mediates direct lipid transfer from ER to IM for IM expansion. Binds to the ER exit site (ERES), which is the membrane source for autophagosome formation, and extracts phospholipids from the membrane source and transfers them to ATG9 (ATG9A or ATG9B) to the IM for membrane expansion. Lipid transfer activity is enhanced by WIPI1 and WDR45/WIPI4, which promote ATG2A-association with phosphatidylinositol 3-monophosphate (PI3P)-containing membranes. Also regulates lipid droplets morphology and distribution within the cell.

Subunit / interactions. Interacts with ATG9A (via C-terminus). Interacts (via WIPI-interacting region) with WDR45B/WIPI3. Interacts (via WIPI-interacting region) with WDR45/WIPI4. Interacts with TMEM41B. Interacts with VMP1.

Subcellular location. Preautophagosomal structure membrane. Lipid droplet. Endoplasmic reticulum membrane.

Domain organisation. The chorein N-terminal domain mediates lipid transfer activity.

Similarity. Belongs to the ATG2 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q2TAZ0-11yes
Q2TAZ0-32
Q2TAZ0-43
Q2TAZ0-54

RefSeq proteins (3): NP_001354900, NP_001354901, NP_055919* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026849ATG2Family

Pfam: PF13329

Catalyzed reactions (Rhea), 2 shown:

  • a 1,2-diacyl-sn-glycero-3-phospho-L-serine(in) = a 1,2-diacyl-sn-glycero-3-phospho-L-serine(out) (RHEA:38663)
  • a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(in) = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine(out) (RHEA:38895)

UniProt features (95 total): strand 25, mutagenesis site 23, helix 11, modified residue 8, turn 7, sequence variant 6, splice variant 5, region of interest 5, compositionally biased region 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
8SBKX-RAY DIFFRACTION1.8
6KLRX-RAY DIFFRACTION2.21
8SBLX-RAY DIFFRACTION3
8KBXELECTRON MICROSCOPY3.23
8KBYELECTRON MICROSCOPY3.23
8KC3ELECTRON MICROSCOPY7
8Y1LELECTRON MICROSCOPY7.05

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2TAZ0-F168.380.18

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): 878, 892, 894, 1266, 1301, 1309, 1402, 765

Mutagenesis-validated functional residues (23):

PositionPhenotype
54in mutant 1; abolished lipid transfer activity; when associated with r-82, e-101, r-167, e-171, r-193, r-200, e-223, r-2
80in mutant 2; abolished lipid transfer activity; when associated with d-103, k-167, r-171, e-193, k-259, e-285 and r-304.
82in mutant 1; abolished lipid transfer activity; when associated with r-54, e-101, r-167, e-171, r-193, r-200, e-223, r-2
101in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, r-167, e-171, r-193, r-200, e-223, r-28
103in mutant 2; abolished lipid transfer activity; when associated with e-80,k-167, r-171, e-193, k-259, e-285 and r-304.
167in mutant 2; abolished lipid transfer activity; when associated with e-80, d-103, r-171, e-193, k-259, e-285 and r-304.
167in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, e-171, r-193, r-200, e-223, r-28
171in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, r-193, r-200, e-223, r-28
171in mutant 2; abolished lipid transfer activity; when associated with e-80, d-103, k-167, e-193, k-259, e-285 and r-304.
193in mutant 2; abolished lipid transfer activity; when associated with e-80, d-103, k-167, r-171, k-259, e-285 and r-304.
193in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, e-171, r-200, e-223, r-28
200in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, e-171, r-193, e-223, r-28
223in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, e-171, r-193, r-200, r-28
259in mutant 2; abolished lipid transfer activity; when associated with e-80, d-103, k-167, r-171, e-193, e-285 and r-304.
285in mutant 2; abolished lipid transfer activity; when associated with e-80, d-103, k-167, r-171, e-193, k-259 and r-304.
285in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, e-171, r-193, r-200, e-22
304in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, e-171, r-193, r-200, e-22
328in mutant 1; abolished lipid transfer activity; when associated with r-54, r-82, e-101, r-167, e-171, r-193, r-200, e-22
1381decreased interaction with wdr45/wipi4 and ability to promote autophagy.
1382decreased interaction with wdr45/wipi4 and ability to promote autophagy.
1389decreased interaction with wdr45/wipi4 and ability to promote autophagy.
1395decreased interaction with wdr45/wipi4 and ability to promote autophagy.
1396decreased interaction with wdr45/wipi4 and ability to promote autophagy.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 172 (showing top): GOBP_REGULATION_OF_AUTOPHAGY, GOBP_VACUOLE_ORGANIZATION, MODULE_255, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_POSITIVE_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MODULE_317, GOBP_REGULATION_OF_VACUOLE_ORGANIZATION, DARWICHE_PAPILLOMA_PROGRESSION_RISK, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, chr11q13, GOBP_MACROAUTOPHAGY, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GOBP_POLYSACCHARIDE_CATABOLIC_PROCESS

GO Biological Process (11): autophagosome assembly (GO:0000045), autophagy of mitochondrion (GO:0000422), pexophagy (GO:0000425), positive regulation of autophagy (GO:0010508), piecemeal microautophagy of the nucleus (GO:0034727), reticulophagy (GO:0061709), glycophagy (GO:0061723), positive regulation of autophagosome assembly (GO:2000786), lipid transport (GO:0006869), autophagy (GO:0006914), intermembrane lipid transfer (GO:0120009)

GO Molecular Function (4): phosphatidylinositol-3-phosphate binding (GO:0032266), protein-membrane adaptor activity (GO:0043495), lipid transfer activity (GO:0120013), protein binding (GO:0005515)

GO Cellular Component (8): phagophore assembly site (GO:0000407), endoplasmic reticulum membrane (GO:0005789), lipid droplet (GO:0005811), phagophore assembly site membrane (GO:0034045), organelle membrane contact site (GO:0044232), phagophore (GO:0061908), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
macroautophagy3
cytoplasm3
autophagy2
Atg12 activating enzyme activity1
protein-phosphatidylethanolamide deconjugating activity1
Atg12 conjugating enzyme activity1
Atg12 ligase activity1
organelle assembly1
Atg1/ULK1 kinase complex assembly1
autophagosome organization1
autophagy of peroxisome1
positive regulation of catabolic process1
regulation of autophagy1
microautophagy1
nucleophagy1
nucleus disassembly1
glycogen catabolic process1
autophagosome assembly1
positive regulation of macroautophagy1
positive regulation of vacuole organization1
positive regulation of organelle assembly1
regulation of autophagosome assembly1
transport1
lipid localization1
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
lipid transport1
membrane organization1
phosphatidylinositol phosphate binding1
protein-macromolecule adaptor activity1
transporter activity1
lipid carrier activity1
intermembrane lipid transfer1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1158 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ATG2AWDR45Q9Y484993
ATG2AWIPI1Q5MNZ9978
ATG2AWIPI2Q9Y4P8910
ATG2AWDR45BQ5MNZ6887
ATG2AATG9AQ7Z3C6868
ATG2AGABARAPO95166866
ATG2AF5GZY7F5GZY7793
ATG2AATG14Q6ZNE5729
ATG2AATG101Q9BSB4716
ATG2AATG12O94817714
ATG2ARB1CC1Q8TDY2710
ATG2AATG10Q9H0Y0709
ATG2AATG3Q9NT62709
ATG2AATG5Q9H1Y0709
ATG2AATG13O75143709

IntAct

48 interactions, top by confidence:

ABTypeScore
ATG2AWDR45psi-mi:“MI:0915”(physical association)0.620
WDR45ATG2Apsi-mi:“MI:0914”(association)0.620
TOMM40ATG2Apsi-mi:“MI:0915”(physical association)0.610
ATG2ATOMM40psi-mi:“MI:0915”(physical association)0.610
ATG2ATOMM40psi-mi:“MI:0914”(association)0.610
ATG2AGABARAPL1psi-mi:“MI:0407”(direct interaction)0.590
GABARAPL1ATG2Apsi-mi:“MI:0915”(physical association)0.590
GABARAPL1IPO5psi-mi:“MI:0914”(association)0.590
ATG2AMEOX2psi-mi:“MI:0915”(physical association)0.560
GABARAPATG2Apsi-mi:“MI:0407”(direct interaction)0.540
GABARAPL2ATG2Apsi-mi:“MI:0407”(direct interaction)0.540
MAP1LC3BATG2Apsi-mi:“MI:0407”(direct interaction)0.540
GABARAPL2ATG2Apsi-mi:“MI:0915”(physical association)0.540
ATG2AGABARAPpsi-mi:“MI:0915”(physical association)0.540
ATG2AMAP1LC3Bpsi-mi:“MI:0915”(physical association)0.540
ATG2AATG9Apsi-mi:“MI:0915”(physical association)0.500
ATG2AMAP1LC3Cpsi-mi:“MI:0407”(direct interaction)0.440
MAP1LC3AATG2Apsi-mi:“MI:0407”(direct interaction)0.440
ATG2AH2BC9psi-mi:“MI:0915”(physical association)0.400
Atg9aATG2Apsi-mi:“MI:0915”(physical association)0.400
WAPLRPL10psi-mi:“MI:0914”(association)0.350
TMEM132AWWP2psi-mi:“MI:0914”(association)0.350
Ewsr1MED24psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
BABAM2RPN2psi-mi:“MI:0914”(association)0.350

BioGRID (55): ATG2A (Affinity Capture-MS), ATG2A (Affinity Capture-MS), ATG2A (Affinity Capture-MS), ATG2A (Affinity Capture-MS), ATG2A (Affinity Capture-MS), ATG2A (Affinity Capture-RNA), ATG2A (Two-hybrid), ATG2A (Affinity Capture-RNA), ATG2A (Proximity Label-MS), ATG2A (Proximity Label-MS), ATG2A (Proximity Label-MS), WDR45 (Reconstituted Complex), WDR45 (Co-crystal Structure), ATG2A (Affinity Capture-MS), ATG2A (Proximity Label-MS)

ESM2 similar proteins: A0A8M9QN10, A0JNW5, A1Z713, A2BID5, A2RRP1, A2RSJ4, B0DOB4, B9EJ80, D3YVL2, D4A039, O70173, O88480, Q08D51, Q14667, Q1LUT1, Q1LXR6, Q21480, Q2TAZ0, Q3UHQ6, Q402B2, Q5H8C4, Q5JWR5, Q5R6T6, Q5SYL3, Q5T0N1, Q5THJ4, Q5TYW4, Q5XIR4, Q642P2, Q6BDS2, Q6INI0, Q6IRN0, Q6NRZ1, Q6P2C0, Q6P4K6, Q6P4T0, Q709C8, Q7ZXT3, Q80XK6, Q8BL99

Diamond homologs: A1CUF9, A1DP40, A2QSC9, A3LT28, A6R6E3, A6S7C7, A7E6F5, A7KAL3, A7TM79, F8S296, I1S0P7, P0CM30, P0CM31, Q08D51, Q0CSI0, Q1E702, Q21480, Q2GYD8, Q2TAZ0, Q2ULE1, Q4WLK5, Q51ZN8, Q5B1T9, Q6C6M0, Q75E74, Q871L5, Q9HFR4, A6ZRK1, P53855, Q6CQ43, Q54KX3, Q6P4T0, Q80XK6, Q96BY7, A1Z713, G0S3B8, Q4PFE7

SIGNOR signaling

2 interactions.

AEffectBMechanism
WDR45“up-regulates activity”ATG2Abinding
ATG2Aup-regulatesAutophagosome_formation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 43 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
Macroautophagy935.8×5e-10

GO biological processes:

GO termPartnersFoldFDR
mitophagy763.6×8e-10
autophagosome maturation660.2×3e-08
autophagosome assembly957.8×3e-12
cellular response to starvation527.7×4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance300
Likely benign24
Benign5

Top pathogenic / likely-pathogenic (0)

SpliceAI

6506 predictions. Top by Δscore:

VariantEffectΔscore
11:64895206:TGCC:Tacceptor_gain1.0000
11:64895207:GCCC:Gacceptor_loss1.0000
11:64895208:CC:Cacceptor_gain1.0000
11:64895209:CC:Cacceptor_gain1.0000
11:64895209:CCT:Cacceptor_loss1.0000
11:64895210:C:CCacceptor_gain1.0000
11:64895210:CT:Cacceptor_loss1.0000
11:64895211:T:Cacceptor_loss1.0000
11:64895286:TCA:Tdonor_loss1.0000
11:64895287:CACCT:Cdonor_loss1.0000
11:64895288:A:Tdonor_loss1.0000
11:64895297:A:ACdonor_gain1.0000
11:64895298:C:CCdonor_gain1.0000
11:64895307:AGG:Adonor_gain1.0000
11:64895439:TGGC:Tacceptor_gain1.0000
11:64895441:GC:Gacceptor_gain1.0000
11:64895442:CC:Cacceptor_gain1.0000
11:64895443:C:CAacceptor_loss1.0000
11:64895443:C:CCacceptor_gain1.0000
11:64895444:T:Cacceptor_loss1.0000
11:64896458:TCA:Tdonor_loss1.0000
11:64896459:CAC:Cdonor_loss1.0000
11:64896460:ACC:Adonor_loss1.0000
11:64896612:TTGGA:Tacceptor_gain1.0000
11:64896613:TGGA:Tacceptor_gain1.0000
11:64896614:GGA:Gacceptor_gain1.0000
11:64896617:C:CCacceptor_gain1.0000
11:64896742:ACTC:Adonor_loss1.0000
11:64896743:CTCA:Cdonor_loss1.0000
11:64896744:TCAC:Tdonor_loss1.0000

AlphaMissense

12443 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:64895435:G:TA1812D1.000
11:64895436:C:GA1812P1.000
11:64896826:A:GW1732R1.000
11:64896826:A:TW1732R1.000
11:64895071:C:GA1907P0.999
11:64895079:G:TA1904D0.999
11:64895193:G:TA1866D0.999
11:64895322:C:GG1850R0.999
11:64896486:G:CS1801R0.999
11:64896486:G:TS1801R0.999
11:64896488:T:GS1801R0.999
11:64896490:A:GL1800P0.999
11:64896499:G:TA1797D0.999
11:64896500:C:GA1797P0.999
11:64896508:G:TA1794D0.999
11:64896532:G:TA1786D0.999
11:64896598:A:GL1764P0.999
11:64897714:A:TI1675N0.999
11:64897732:A:GF1669S0.999
11:64897738:A:GF1667S0.999
11:64898301:A:GL1578P0.999
11:64898754:C:GR1518P0.999
11:64901995:G:CF1362L0.999
11:64901995:G:TF1362L0.999
11:64901997:A:GF1362L0.999
11:64895058:A:GL1911P0.998
11:64895080:C:GA1904P0.998
11:64895091:G:CP1900R0.998
11:64895184:A:TI1869N0.998
11:64895194:C:GA1866P0.998

dbSNP variants (sampled 300 via entrez): RS1000041199 (11:64918129 C>T), RS1000132720 (11:64900722 G>A), RS1000497536 (11:64917806 G>A), RS1000775364 (11:64916809 G>A,T), RS1000847365 (11:64896141 C>A,T), RS1001008060 (11:64901721 C>G,T), RS1001121458 (11:64906723 G>C), RS1001124227 (11:64916395 G>A,T), RS1001196162 (11:64896355 C>G,T), RS1001222718 (11:64907214 G>A), RS1001376659 (11:64912742 T>A,C), RS1001525857 (11:64918623 G>A,T), RS1001828126 (11:64912464 C>G,T), RS1001969206 (11:64900820 T>C), RS1002281928 (11:64917283 GCTCA>G)

Disease associations

OMIM: gene MIM:616225 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary ovarian failure (MONDO:0005387)

Orphanet (1): NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST003264_467Post bronchodilator FEV1/FVC ratio3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004713FEV/FVC ratio

MeSH disease descriptors (1)

DescriptorNameTree numbers
D016649Primary Ovarian InsufficiencyC12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression, affects cotreatment4
Arsenicincreases methylation, affects cotreatment, decreases expression, increases abundance, increases expression3
Air Pollutantsaffects expression, affects cotreatment, decreases expression, increases abundance2
Ozoneaffects expression, affects cotreatment, decreases expression, increases abundance2
Tobacco Smoke Pollutionaffects expression, increases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneincreases abundance, affects cotreatment, decreases expression1
trichostatin Aaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
trovafloxacinaffects cotreatment, increases expression1
abrineincreases expression1
Zoledronic Acidincreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Azathioprineincreases expression1
Caffeineaffects phosphorylation1
Doxorubicindecreases expression1
Quercetinincreases expression1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Thiramincreases expression1
Tretinoinincreases expression1
Urethaneincreases expression1
Valproic Acidincreases methylation1
Cyclosporineincreases expression1
Acrylamidedecreases expression1

Cellosaurus cell lines

16 cell lines: 10 cancer cell line, 6 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B1KIAbcam HeLa ATG2A KOCancer cell lineFemale
CVCL_E1R8HAP1 ATG2A (-) 1Cancer cell lineMale
CVCL_E1R9HAP1 ATG2A (-) 2Cancer cell lineMale
CVCL_E1RAHAP1 ATG2A (-) 3Cancer cell lineMale
CVCL_E1RBHAP1 ATG2A (-) 4Cancer cell lineMale
CVCL_E1RCHAP1 ATG2A (-) 5Cancer cell lineMale
CVCL_E8CGHEK293 ATG2A/ATG2B DKOTransformed cell lineFemale
CVCL_E8CHHEK293 ATG2A/2B DKO GFP-ATG2ATransformed cell lineFemale
CVCL_E8CIHEK293 ATG2A/2B DKO GFP-ATG2A(1-345)Transformed cell lineFemale
CVCL_E8CJHEK293 ATG2A/2B DKO GFP-ATG2A(del1-345)Transformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00417066PHASE4COMPLETEDFlexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693PHASE4COMPLETEDEvaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616PHASE4COMPLETEDEstrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501PHASE4UNKNOWNEffects of ADSC Therapy in Women With POF
NCT02783937PHASE4COMPLETEDFilgrastim for Premature Ovarian Insufficiency
NCT03535480PHASE4UNKNOWNAutologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT00140998PHASE3COMPLETEDEstrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT00001951PHASE2COMPLETEDHormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019PHASE2WITHDRAWNEffects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494PHASE2COMPLETEDGnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852PHASE2SUSPENDEDThe Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467PHASE2UNKNOWNPrevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982PHASE2COMPLETEDThe Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
NCT02912104PHASE1COMPLETEDA Therapeutic Trial of Human Amniotic Epithelial Cells Transplantation for Primary Ovarian Failure
NCT03178695PHASE1COMPLETEDInovium Ovarian Rejuvenation Trials
NCT04815213PHASE1ACTIVE_NOT_RECRUITINGThe Use of Expandeded Mesenchymal Stromal Cells (MSC) in Premature Ovarian Failure (POF) in Adult Humans
NCT05138367PHASE1COMPLETEDEffects of UCA-PSCs in Women With POF
NCT06132542PHASE1UNKNOWNAutologous ADMSC Transplantation in Patients With POI
NCT00948857PHASE2/PHASE3TERMINATEDDehydroepiandrosterone (DHEA) Treatment and Premature Ovarian Failure (POF)
NCT04031456PHASE2/PHASE3RECRUITINGAutologous PRP Infusion May Restore Ovarian Function and May Promote Folliculogenesis in POI Patients
NCT02043743PHASE1/PHASE2UNKNOWNAutologous Stem Cells Transplantation in Patients With Idiopathic and Drug Induced Premature Ovarian Failure
NCT02062931PHASE1/PHASE2UNKNOWNAutologous Mesenchymal Stem Cells Transplantation In Women With Premature Ovarian Failure
NCT02151890PHASE1/PHASE2COMPLETEDPregnancy After Stem Cell Transplantation in Premature Ovarian Failure
NCT02372474PHASE1/PHASE2COMPLETEDIt is a Real The First Baby Of Autologous Stem Cell Therapy in Premature Ovarian Failure
NCT02603744PHASE1/PHASE2UNKNOWNAutologous Adipose Derived Mesenchymal Stromal Cells Transplantation in Women With Premature Ovarian Failure (POF)
NCT02644447PHASE1/PHASE2COMPLETEDTransplantation of HUC-MSCs With Injectable Collagen Scaffold for POF
NCT03069209PHASE1/PHASE2UNKNOWNAutologous Bone Marrow-Derived Stem Cell Transplantation in Patients With Premature Ovarian Failure (POF)
NCT03985462PHASE1/PHASE2WITHDRAWNVery Small Embryonic-like Stem Cells for Ovary
NCT04009473PHASE1/PHASE2UNKNOWNStem Cell Therapy and Growth Factor Ovarian in Vitro Activation
NCT04071574PHASE1/PHASE2COMPLETEDComparative Study on the Efficacy of Ovarian Stimulation Protocols on the Success Rate of ICSI in Female Infertility
NCT04922398PHASE1/PHASE2UNKNOWNOvarian Injection of PRP (Platelet -Rich Plasma) Vs Normal Saline in Premature Ovarian Insufficiency
NCT05462379PHASE1/PHASE2ACTIVE_NOT_RECRUITINGAutologous Heterotopic Fresh Ovarian Graft in Woman With LACC Eligible for Pelvic Radiotherapy Treatment.
NCT06202547PHASE1/PHASE2UNKNOWNIntra-ovarian Injection of MSC-EVs in Idiopathic Premature Ovarian Failure
NCT01129947EARLY_PHASE1WITHDRAWNThe Use of DHEA in Women With Premature Ovarian Failure
NCT05522634EARLY_PHASE1UNKNOWNA Clinical Study of Chinese Herbal Compound TJAOA101 in the Treatment of Premature Ovarian Insufficiency
NCT07308327EARLY_PHASE1ACTIVE_NOT_RECRUITINGThe Influence of Gut Microbiota on Ovarian Function: A Single-center, Randomized,Double Blind, Parallel-controlled, Exploratory Clinical Trial
NCT00001275Not specifiedCOMPLETEDOvarian Follicle Function in Patients With Primary Ovarian Failure
NCT00001306Not specifiedCOMPLETEDSteroid Therapy in Autoimmune Premature Ovarian Failure
NCT00006156Not specifiedCOMPLETEDFeasibility Study for Development of an Early Test for Ovarian Failure
NCT00119925Not specifiedUNKNOWN‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot