ATG2B

Summary

ATG2B (autophagy related 2B, HGNC:20187) is a protein-coding gene on chromosome 14q32.2, encoding Autophagy-related protein 2 homolog B (Q96BY7). Lipid transfer protein required for both autophagosome formation and regulation of lipid droplet morphology and dispersion.

This gene encodes a protein required for autophagy. The encoded protein is involved in autophagosome formation. A germline duplication of a region that includes this gene is associated with predisposition to myeloid malignancies.

Source: NCBI Gene 55102 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 423 total
• MANE Select transcript: NM_018036

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20187
Approved symbol	ATG2B
Name	autophagy related 2B
Location	14q32.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10242, BLTP4B
Ensembl gene	ENSG00000066739
Ensembl biotype	protein_coding
OMIM	616226
Entrez	55102

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding_CDS_not_defined, 2 protein_coding, 2 retained_intron

ENST00000261834, ENST00000359933, ENST00000473234, ENST00000488421, ENST00000553643, ENST00000554151, ENST00000555263, ENST00000938845

RefSeq mRNA: 1 — MANE Select: NM_018036 NM_018036

CCDS: CCDS9944

Canonical transcript exons

ENST00000359933 — 42 exons

Exon	Start	End
ENSE00000660135	96289656	96289805
ENSE00001204283	96279195	96285985
ENSE00001593019	96313329	96313435
ENSE00001611529	96328347	96328535
ENSE00001626298	96333688	96333873
ENSE00001629522	96334405	96334501
ENSE00001636412	96322112	96322254
ENSE00001644920	96315384	96315583
ENSE00001654027	96311117	96311287
ENSE00001686943	96328674	96328766
ENSE00001699544	96317145	96317317
ENSE00001702282	96332305	96332410
ENSE00001702949	96343119	96343281
ENSE00001707953	96344654	96344756
ENSE00001708630	96317698	96317855
ENSE00001711665	96316533	96316683
ENSE00001713774	96312089	96312159
ENSE00001745211	96313065	96313157
ENSE00001747882	96315154	96315234
ENSE00001748386	96345233	96345385
ENSE00001751473	96311542	96311618
ENSE00001751770	96341522	96341701
ENSE00001759076	96331376	96331637
ENSE00001768544	96325649	96325922
ENSE00001799994	96347179	96347341
ENSE00001803065	96332501	96332655
ENSE00001806658	96329484	96329634
ENSE00001915512	96362815	96363341
ENSE00003464784	96322540	96322735
ENSE00003472468	96292029	96292098
ENSE00003481530	96309453	96309594
ENSE00003527565	96290814	96290935
ENSE00003552673	96323896	96323998
ENSE00003565663	96306714	96306916
ENSE00003615912	96294960	96295167
ENSE00003639898	96303061	96303255
ENSE00003640285	96304495	96304603
ENSE00003647037	96295482	96295560
ENSE00003654256	96302007	96302108
ENSE00003657686	96290436	96290590
ENSE00003670200	96305589	96305815
ENSE00003693681	96291600	96291682

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 96.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5937 / max 162.8225, expressed in 1761 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
144811	6.2561	1693
144810	4.7290	1339
144809	0.4309	209
144808	0.1778	75

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	96.74	gold quality
middle temporal gyrus	UBERON:0002771	96.52	gold quality
sperm	CL:0000019	96.01	gold quality
endothelial cell	CL:0000115	95.29	gold quality
upper leg skin	UBERON:0004262	94.05	gold quality
tibia	UBERON:0000979	93.70	gold quality
skin of hip	UBERON:0001554	93.27	gold quality
sural nerve	UBERON:0015488	92.60	gold quality
body of pancreas	UBERON:0001150	92.26	gold quality
male germ cell	CL:0000015	92.01	gold quality
calcaneal tendon	UBERON:0003701	91.36	gold quality
gingival epithelium	UBERON:0001949	91.35	gold quality
postcentral gyrus	UBERON:0002581	91.02	gold quality
visceral pleura	UBERON:0002401	90.31	gold quality
colonic epithelium	UBERON:0000397	90.21	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	90.17	gold quality
corpus callosum	UBERON:0002336	90.04	gold quality
skin of abdomen	UBERON:0001416	90.01	gold quality
trabecular bone tissue	UBERON:0002483	90.01	gold quality
skin of leg	UBERON:0001511	89.91	gold quality
parietal lobe	UBERON:0001872	89.89	gold quality
substantia nigra pars compacta	UBERON:0001965	89.79	gold quality
parietal pleura	UBERON:0002400	89.67	gold quality
adrenal tissue	UBERON:0018303	89.54	gold quality
entorhinal cortex	UBERON:0002728	89.49	gold quality
biceps brachii	UBERON:0001507	89.45	gold quality
pons	UBERON:0000988	89.33	gold quality
lateral nuclear group of thalamus	UBERON:0002736	89.25	gold quality
superior frontal gyrus	UBERON:0002661	89.16	gold quality
pleura	UBERON:0000977	89.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.56

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

172 targeting ATG2B, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-381-3P	99.93	71.87	2854

Literature-anchored findings (GeneRIF, showing 23)

• 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)
• miR-130a inhibited autophagy by reducing autophagosome formation, an effect mediated by downregulation of the genes ATG2B and DICER1. (PMID:22350415)
• miR-143 inhibits cell proliferation by targeting autophagy-related 2B in non-small cell lung cancer H1299 cells. (PMID:25322940)
• demonstrate that overexpression of ATG2B and GSKIP enhances hematopoietic progenitor differentiation, including of megakaryocytes, by increasing progenitor sensitivity to thrombopoietin (PMID:26280900)
• This study highlights the transcriptional inactivation mechanisms of ATG2B, ATG4D, ATG9A and ATG9B promoter methylation status and the possible origin of autophagy signal pathway repression in invasive ductal carcinomas. (PMID:27265029)
• Our results suggest that these three genes that are critical components of the autophagy pathway (ATG16L, ATG2B, ATG5) are not significant risk factors among Spanish patients with either pseudoexfoliation syndrome or pseudoexfoliation glaucoma. (PMID:27960588)
• 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)
• miR-143 may induce bowel inflammation by regulating ATG2B and autophagy, suggesting that miR-143 might play a critical role in the development of Crohn’s Disease (PMID:29562274)
• A conserved ATG2-GABARAP family interaction is critical for phagophore formation. (PMID:32009292)
• MicroRNA-375 exacerbates knee osteoarthritis through repressing chondrocyte autophagy by targeting ATG2B. (PMID:32335541)
• miR-1278 sensitizes nasopharyngeal carcinoma cells to cisplatin and suppresses autophagy via targeting ATG2B. (PMID:32407879)
• miR-375 targeting autophagy-related 2B (ATG2B) suppresses autophagy and tumorigenesis in cisplatin-resistant osteosarcoma cells. (PMID:32726125)
• MiR-143-3p targets ATG2B to inhibit autophagy and promote endothelial progenitor cells tube formation in deep vein thrombosis. (PMID:33130456)
• Polymorphism in autophagy gene ATG2B is not associated with bladder cancer recurrence after intravesical Bacillus Calmette-Guerin (BCG) immunotherapy in Asian patients. (PMID:33250346)
• ATG2B/GSKIP in de novo acute myeloid leukemia (AML): high prevalence of germline predisposition in French West Indies. (PMID:33554699)
• miR1433p inhibits endometriotic stromal cell proliferation and invasion by inactivating autophagy in endometriosis. (PMID:33760149)
• LncRNA-HOTAIR activates autophagy and promotes the imatinib resistance of gastrointestinal stromal tumor cells through a mechanism involving the miR-130a/ATG2B pathway. (PMID:33824300)
• Germline ATG2B/GSKIP-containing 14q32 duplication predisposes to early clonal hematopoiesis leading to myeloid neoplasms. (PMID:34172895)
• Crocin exerts anti-proliferative and apoptotic effects on cutaneous squamous cell carcinoma via miR-320a/ATG2B. (PMID:34320900)
• Downregulation of LINC01296 suppresses non-small-cell lung cancer via targeting miR-143-3p/ATG2B. (PMID:34695177)
• Loss of Atg2b and Gskip Impairs the Maintenance of the Hematopoietic Stem Cell Pool Size. (PMID:34748402)
• The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma. (PMID:35902797)
• Human gastric cancer progression and stabilization of ATG2B through RNF5 binding facilitated by autophagy-associated CircDHX8. (PMID:38866787)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	atg2b	ENSDARG00000097650
mus_musculus	Atg2b	ENSMUSG00000041341
rattus_norvegicus	Atg2b	ENSRNOG00000004519
drosophila_melanogaster	Atg2	FBGN0044452
caenorhabditis_elegans		WBGENE00019748

Paralogs (1): ATG2A (ENSG00000110046)

Protein

Protein identifiers

Autophagy-related protein 2 homolog B — Q96BY7 (reviewed: Q96BY7)

All UniProt accessions (1): Q96BY7

UniProt curated annotations — full annotation on UniProt →

Function. Lipid transfer protein required for both autophagosome formation and regulation of lipid droplet morphology and dispersion. 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 WDR45/WIPI4, which promotes ATG2B-association with phosphatidylinositol 3-monophosphate (PI3P)-containing membranes.

Subunit / interactions. Interacts with WDR45/WIPI4.

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.

RefSeq proteins (1): NP_060506* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026849	ATG2	Family

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 (27 total): modified residue 12, sequence conflict 4, sequence variant 3, region of interest 3, compositionally biased region 2, chain 1, domain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96BY7-F1	65.72	0.16

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 (12): 840, 886, 899, 1008, 1012, 1016, 1018, 1022, 1526, 255, 379, 497

Mutagenesis-validated functional residues (1):

Position	Phenotype
1025–1027	strongly reduced interaction with wdr45/wipi4.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): RNGTGGGC_UNKNOWN, GOBP_VACUOLE_ORGANIZATION, GCM_GSPT1, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_MACROAUTOPHAGY, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GOBP_POLYSACCHARIDE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_ORGANELLE_ASSEMBLY, GOBP_CARBOHYDRATE_CATABOLIC_PROCESS, GCM_NF2, GOBP_MEMBRANE_ORGANIZATION, GOBP_LIPID_LOCALIZATION, chr14q32, GOBP_AUTOPHAGOSOME_ORGANIZATION

GO Biological Process (9): autophagosome assembly (GO:0000045), autophagy of mitochondrion (GO:0000422), pexophagy (GO:0000425), piecemeal microautophagy of the nucleus (GO:0034727), reticulophagy (GO:0061709), glycophagy (GO:0061723), 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 (7): phagophore assembly site (GO:0000407), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), lipid droplet (GO:0005811), phagophore assembly site membrane (GO:0034045), phagophore (GO:0061908), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
macroautophagy	3
cytoplasm	3
cellular anatomical structure	3
Atg12 activating enzyme activity	1
protein-phosphatidylethanolamide deconjugating activity	1
Atg12 conjugating enzyme activity	1
Atg12 ligase activity	1
organelle assembly	1
Atg1/ULK1 kinase complex assembly	1
autophagosome organization	1
autophagy	1
autophagy of peroxisome	1
microautophagy	1
nucleophagy	1
nucleus disassembly	1
glycogen catabolic process	1
transport	1
lipid localization	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
lipid transport	1
membrane organization	1
phosphatidylinositol phosphate binding	1
protein-macromolecule adaptor activity	1
transporter activity	1
lipid carrier activity	1
intermembrane lipid transfer	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
intracellular membraneless organelle	1
phagophore assembly site	1
membrane	1

Protein interactions and networks

STRING

1496 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATG2B	WDR45	Q9Y484	984
ATG2B	WIPI1	Q5MNZ9	929
ATG2B	WIPI2	Q9Y4P8	804
ATG2B	GSKIP	Q9P0R6	783
ATG2B	WDR45B	Q5MNZ6	774
ATG2B	ATG9B	Q674R7	772
ATG2B	F5GZY7	F5GZY7	767
ATG2B	ATG5	Q9H1Y0	742
ATG2B	ATG12	O94817	726
ATG2B	ATG10	Q9H0Y0	725
ATG2B	GABARAP	O95166	723
ATG2B	ATG9A	Q7Z3C6	716
ATG2B	ATG7	O95352	708
ATG2B	ATG14	Q6ZNE5	703
ATG2B	ATG3	Q9NT62	690
ATG2B	ATG4C	Q96DT6	690

IntAct

80 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
ATG2B	WDR45	psi-mi:“MI:0915”(physical association)	0.730
HDAC11	CLUH	psi-mi:“MI:0914”(association)	0.640
WDR45	ATG2A	psi-mi:“MI:0914”(association)	0.620
NPAS1	DNAJB5	psi-mi:“MI:0914”(association)	0.530
SKP2	DPYSL4	psi-mi:“MI:0914”(association)	0.530
MLF1	NDC80	psi-mi:“MI:0914”(association)	0.530
BRINP3	BUB1	psi-mi:“MI:0914”(association)	0.530
SALL2	GFPT2	psi-mi:“MI:0914”(association)	0.530
ATG2B	TKT	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
MAP1LC3B	ATG2B	psi-mi:“MI:0407”(direct interaction)	0.440
GSK3B	SEC16A	psi-mi:“MI:2364”(proximity)	0.420
ATG2B	PDIA6	psi-mi:“MI:0915”(physical association)	0.400
ZSCAN26	TDG	psi-mi:“MI:0914”(association)	0.350
PB1	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
PB1		psi-mi:“MI:0914”(association)	0.350
PB2	IPO5	psi-mi:“MI:0914”(association)	0.350
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
C6orf141	KRBA1	psi-mi:“MI:0914”(association)	0.350
AP1G2	ZNF318	psi-mi:“MI:0914”(association)	0.350

BioGRID (123): ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Proximity Label-MS), ATG2B (Proximity Label-MS), ATG2B (Proximity Label-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), WDR45 (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS), ATG2B (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IXF6, A0JMR6, A0JNW5, A2RSJ4, F4HRV8, O17482, O95876, P49021, P79457, Q08D51, Q28C33, Q3B7T1, Q3UD82, Q498F0, Q5H8C4, Q5JSH3, Q5JTW2, Q5QNQ6, Q5R9R1, Q5THJ4, Q5ZLG9, Q6BDS2, Q6GLR7, Q6GQV7, Q6INA9, Q6NRZ1, Q6NVE8, Q6ZMT4, Q6ZWJ1, Q709C8, Q80T23, Q80XK6, Q812E4, Q8BX70, Q8BXR9, Q8C5W4, Q8IWB9, Q8N3A8, Q8N7X0, Q8TDW5

Diamond homologs: Q08D51, Q2TAZ0, Q54KX3, Q6P4T0, Q80XK6, Q96BY7, P0CM30, P0CM31, Q21480

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
WDR45	“up-regulates activity”	ATG2B	binding
ATG2B	up-regulates	Autophagosome_formation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 96 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
Activation of the pre-replicative complex	5	27.6×	4e-05
DNA Replication Pre-Initiation	5	26.9×	4e-05
Activation of ATR in response to replication stress	5	25.5×	4e-05
Switching of origins to a post-replicative state	5	25.5×	4e-05
Synthesis of DNA	5	25.5×	4e-05
DNA Replication	6	24.2×	1e-05
G1/S Transition	6	23.7×	1e-05
Mitotic G1 phase and G1/S transition	6	18.7×	4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	253
Likely benign	40
Benign	94

Top pathogenic / likely-pathogenic (0)

SpliceAI

6349 predictions. Top by Δscore:

Variant	Effect	Δscore
14:96289812:CA:C	acceptor_gain	1.0000
14:96289813:A:T	acceptor_gain	1.0000
14:96289816:T:C	acceptor_gain	1.0000
14:96289816:T:TC	acceptor_gain	1.0000
14:96289820:C:CT	acceptor_gain	1.0000
14:96290591:C:CC	acceptor_gain	1.0000
14:96290809:CTCA:C	donor_loss	1.0000
14:96290810:TCA:T	donor_loss	1.0000
14:96290811:CACCT:C	donor_loss	1.0000
14:96290812:A:AC	donor_gain	1.0000
14:96290812:ACC:A	donor_loss	1.0000
14:96290813:C:CA	donor_loss	1.0000
14:96290813:C:CC	donor_gain	1.0000
14:96290813:CCT:C	donor_gain	1.0000
14:96290813:CCTA:C	donor_gain	1.0000
14:96290813:CCTAA:C	donor_gain	1.0000
14:96290936:C:CC	acceptor_gain	1.0000
14:96291594:ACTT:A	donor_loss	1.0000
14:96291595:CTTA:C	donor_loss	1.0000
14:96291596:TTACC:T	donor_loss	1.0000
14:96291597:TA:T	donor_loss	1.0000
14:96291598:A:AC	donor_gain	1.0000
14:96291598:A:AT	donor_loss	1.0000
14:96291598:AC:A	donor_gain	1.0000
14:96291599:C:CC	donor_gain	1.0000
14:96291599:CC:C	donor_gain	1.0000
14:96291681:CC:C	acceptor_gain	1.0000
14:96291682:CC:C	acceptor_gain	1.0000
14:96291686:C:CT	acceptor_gain	1.0000
14:96295466:TA:T	donor_gain	1.0000

AlphaMissense

13646 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:96289799:C:G	A1955P	1.000
14:96290892:A:G	W1875R	1.000
14:96290892:A:T	W1875R	1.000
14:96305653:A:G	W1557R	1.000
14:96305653:A:T	W1557R	1.000
14:96347257:A:G	W83R	1.000
14:96347257:A:T	W83R	1.000
14:96285847:C:G	A2049P	0.999
14:96285855:G:T	A2046D	0.999
14:96285856:C:G	A2046P	0.999
14:96285969:G:T	A2008D	0.999
14:96289688:C:G	G1992R	0.999
14:96289789:G:T	A1958D	0.999
14:96290440:A:T	I1951K	0.999
14:96290464:A:G	L1943P	0.999
14:96290474:C:G	A1940P	0.999
14:96290521:C:T	G1924E	0.999
14:96290522:C:G	G1924R	0.999
14:96290522:C:T	G1924R	0.999
14:96291645:A:G	L1845S	0.999
14:96291657:C:T	G1841D	0.999
14:96292058:A:C	Y1823D	0.999
14:96292069:A:T	I1819N	0.999
14:96292087:A:G	F1813S	0.999
14:96302020:A:G	L1709P	0.999
14:96317833:A:G	W968R	0.999
14:96317833:A:T	W968R	0.999
14:96328438:C:A	R691M	0.999
14:96345241:A:T	I157N	0.999
14:96345250:G:T	A154D	0.999

dbSNP variants (sampled 300 via entrez): RS1000047617 (14:96353595 C>T), RS1000169867 (14:96281917 G>A), RS1000218978 (14:96291820 T>C), RS1000234409 (14:96287058 A>G), RS1000339339 (14:96323432 C>T), RS1000342484 (14:96299425 A>G), RS1000350868 (14:96364815 C>G), RS1000391938 (14:96280469 T>C), RS1000394848 (14:96299648 T>C), RS1000408770 (14:96363356 C>A), RS1000434253 (14:96323681 G>A), RS1000497547 (14:96303631 A>T), RS1000503267 (14:96293170 T>C), RS1000521194 (14:96347043 G>C), RS1000560721 (14:96327621 T>C)

Disease associations

OMIM: gene MIM:616226 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004720_9	Conotruncal heart defects (inherited effects)	5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases methylation	2
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
oxybenzone	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
arsenite	affects binding, decreases reaction	1
butyraldehyde	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
trovafloxacin	increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases response to substance, increases expression	1
(+)-JQ1 compound	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Caffeine	affects phosphorylation	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Manganese	decreases expression, increases abundance	1
Methotrexate	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Progesterone	increases expression	1
Thimerosal	decreases expression	1

Cellosaurus cell lines

14 cell lines: 8 cancer cell line, 6 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1KJ	Abcam HeLa ATG2B KO	Cancer cell line	Female
CVCL_E1RD	HAP1 ATG2B (-) 1	Cancer cell line	Male
CVCL_E1RE	HAP1 ATG2B (-) 2	Cancer cell line	Male
CVCL_E1RF	HAP1 ATG2B (-) 3	Cancer cell line	Male
CVCL_E8CG	HEK293 ATG2A/ATG2B DKO	Transformed cell line	Female
CVCL_E8CH	HEK293 ATG2A/2B DKO GFP-ATG2A	Transformed cell line	Female
CVCL_E8CI	HEK293 ATG2A/2B DKO GFP-ATG2A(1-345)	Transformed cell line	Female
CVCL_E8CJ	HEK293 ATG2A/2B DKO GFP-ATG2A(del1-345)	Transformed cell line	Female
CVCL_E8GU	HEK293 ATG2A/ATG2B DKO APEX2-EGFP-ATG2A	Transformed cell line	Female
CVCL_E8GV	HEK293 ATG2A/ATG2B DKO GFP-ATG2A TagBFP-LC3B	Transformed cell line	Female

Clinical trials (associated diseases)

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