AMBRA1

Summary

AMBRA1 (autophagy and beclin 1 regulator 1, HGNC:25990) is a protein-coding gene on chromosome 11p11.2, encoding Activating molecule in BECN1-regulated autophagy protein 1 (Q9C0C7). Substrate-recognition component of a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex involved in cell cycle control and autophagy. It is a selective cancer dependency (DepMap: 15.0% of cell lines).

Enables enzyme binding activity; protein phosphatase activator activity; and ubiquitin-like ligase-substrate adaptor activity. Involved in several processes, including macroautophagy; positive regulation of free ubiquitin chain polymerization; and positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction. Located in cytosol. Part of Cul4-RING E3 ubiquitin ligase complex. Is active in cytoskeleton; mitochondrion; and nucleus. Biomarker of multiple system atrophy.

Source: NCBI Gene 55626 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neural tube defects, susceptibility to (Strong, GenCC)
• GWAS associations: 15
• Clinical variants (ClinVar): 197 total
• Phenotypes (HPO): 2
• Cancer dependency (DepMap): dependent in 15.0% of screened cell lines
• MANE Select transcript: NM_001387011

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25990
Approved symbol	AMBRA1
Name	autophagy and beclin 1 regulator 1
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20294, KIAA1736, WDR94, DCAF3
Ensembl gene	ENSG00000110497
Ensembl biotype	protein_coding
OMIM	611359
Entrez	55626

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 19 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000314845, ENST00000458649, ENST00000524783, ENST00000526545, ENST00000526606, ENST00000528950, ENST00000529553, ENST00000529558, ENST00000529963, ENST00000531542, ENST00000533727, ENST00000534300, ENST00000683756, ENST00000878706, ENST00000878707, ENST00000878708, ENST00000935632, ENST00000935633, ENST00000935634, ENST00000935635, ENST00000935636, ENST00000935637, ENST00000953643, ENST00000953644

RefSeq mRNA: 9 — MANE Select: NM_001387011 NM_001267782, NM_001267783, NM_001300731, NM_001367468, NM_001367469, NM_001367470, NM_001367471, NM_001387011, NM_017749

CCDS: CCDS31475, CCDS58132, CCDS73281, CCDS91466

Canonical transcript exons

ENST00000683756 — 18 exons

Exon	Start	End
ENSE00000989227	46545604	46545776
ENSE00001181736	46543975	46544041
ENSE00001181742	46547113	46547296
ENSE00001233738	46433474	46433628
ENSE00001294054	46541945	46543398
ENSE00001618405	46410276	46410368
ENSE00001632697	46408513	46408706
ENSE00001726167	46396414	46397943
ENSE00002310931	46417913	46418052
ENSE00003468872	46434849	46435037
ENSE00003550468	46493608	46493708
ENSE00003565359	46548246	46548500
ENSE00003575382	46508191	46508370
ENSE00003576784	46512727	46512813
ENSE00003596802	46547817	46547875
ENSE00003687022	46494124	46494204
ENSE00003687588	46443488	46443598
ENSE00003916724	46593828	46594023

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 93.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.0809 / max 197.0913, expressed in 1821 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119521	33.7586	1821
119523	0.2407	36
119524	0.0626	22
119522	0.0190	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	93.04	gold quality
secondary oocyte	CL:0000655	92.25	gold quality
cervix squamous epithelium	UBERON:0006922	91.00	silver quality
adrenal tissue	UBERON:0018303	90.58	gold quality
vena cava	UBERON:0004087	89.26	silver quality
tendon of biceps brachii	UBERON:0008188	88.81	gold quality
nipple	UBERON:0002030	88.25	gold quality
pharyngeal mucosa	UBERON:0000355	87.74	gold quality
cortical plate	UBERON:0005343	87.61	gold quality
cerebellar vermis	UBERON:0004720	87.41	silver quality
cardia of stomach	UBERON:0001162	87.11	silver quality
ventral tegmental area	UBERON:0002691	87.01	gold quality
thymus	UBERON:0002370	86.92	gold quality
pylorus	UBERON:0001166	86.79	gold quality
pericardium	UBERON:0002407	86.68	gold quality
trachea	UBERON:0003126	86.61	gold quality
saphenous vein	UBERON:0007318	86.49	gold quality
right adrenal gland cortex	UBERON:0035827	86.46	gold quality
colonic epithelium	UBERON:0000397	86.39	gold quality
pons	UBERON:0000988	86.28	silver quality
trigeminal ganglion	UBERON:0001675	86.28	gold quality
adrenal gland	UBERON:0002369	86.23	gold quality
inferior vagus X ganglion	UBERON:0005363	86.19	gold quality
pancreatic ductal cell	CL:0002079	86.17	gold quality
subthalamic nucleus	UBERON:0001906	86.17	gold quality
adrenal cortex	UBERON:0001235	86.09	gold quality
left adrenal gland	UBERON:0001234	85.97	gold quality
lateral globus pallidus	UBERON:0002476	85.95	gold quality
dorsal plus ventral thalamus	UBERON:0001897	85.88	gold quality
left adrenal gland cortex	UBERON:0035825	85.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting AMBRA1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
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-1236-3P	99.94	68.04	1695
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• When autophagy is induced, ULK1 phosphorylates AMBRA1, releasing the autophagy core complex from dynein. (PMID:20921139)
• In this study, the authors show that AMBRA1 binds preferentially the mitochondrial pool of the antiapoptotic factor BCL-2, and that this interaction is disrupted following autophagy induction. (PMID:21358617)
• Ambra1 is an important target of apoptotic proteases resulting in the dismantling of the autophagic machinery and the accomplishment of the cell death program (PMID:22441670)
• role that Ambra1 in the switch between autophagy and apoptosis (PMID:23069654)
• Data suggest that activated autophagy is associated with the progression of pancreatic ductal adenocarcinoma and that the overexpression of autophagy-related proteins Atg5, Ambra1, beclin-1, LC3B and Bif-1 is significantly correlated with poor outcome. (PMID:23429496)
• findings show under non-autophagic conditions, mTOR inhibits AMBRA1 by phosphorylation, whereas on autophagy induction, AMBRA1 is dephosphorylated; in this condition, AMBRA1, interacting with TRAF6, supports ULK1 ubiquitylation by LYS-63-linked chains, and its stabilization, self-association and function (PMID:23524951)
• A schizophrenia-related risk variant in AMBRA1 (rs11819869) is involved in various aspects of impulsivity, and this involvement occurs on a behavioral as well as an imaging genetics level. (PMID:23551272)
• Ambra1 is a crucial regulator of autophagy and apoptosis in colorectal cancer cells (PMID:24587252)
• a de-regulation of c-Myc correlates with increased tumorigenesis in AMBRA1-defective systems, thus supporting a role for AMBRA1 as a haploinsufficient tumour suppressor gene. (PMID:25438055)
• AMBRA1 interacts with cullin E3 ubiquitin ligases to regulate autophagy dynamics (PMID:25499913)
• Both AMBRA1 and BECLIN 1 affect c-Myc regulation, but through two different pathways. (PMID:25803737)
• Ambra1 mRNA translocation to P-bodies and translational suppression correlated with increased cell death. (PMID:26086269)
• An increased expression of AMBRA1 and SQSTM1. (PMID:26423274)
• Ambra1 is a crucial regulator of autophagy and apoptosis in ovarian cancer cells subject to cisplatin to maintain the balance between autophagy and apoptosis. Ambra1-targeting inhibition might sensitize ovarian cancer cells to chemotherapy. (PMID:26763392)
• Results showed that AMBRA1 is a novel hub binding protein of alpha-synuclein and plays a central role in the pathogenesis of multiple system atrophy through the degradative dynamics of alpha-synuclein. (PMID:27875637)
• These data suggest a new and interesting role of MIR7-3HG as an anti-autophagic MIRNA that may affect oncogenesis through the regulation of the tumor suppressor AMBRA1. (PMID:28059583)
• Results show that the expression of AMBRA1 and Beclin-1 is increased in human gastric adenocarcinoma (GC) tissues. High protein expression of AMBRA1 and Beclin-1 is correlated with tumor invasion and is an independent poor prognostic marker in GC patients. (PMID:28224423)
• Data support a role of AMBRA1/Ambra1 partial loss-of-function genotypes for female autistic traits. Moreover, they suggest Ambra1 heterozygous mice as a novel multifaceted and construct-valid genetic mouse model for female autism. (PMID:28994820)
• Ambra1 induces autophagy and desensitizes human prostate cancer cells to cisplatin. (PMID:29101240)
• Ambra1 plays an important role in regulating the sensitivity of breast cancer cells to epirubicin. Regulatory effect of Ambra1 on epirubicin sensitivity is achieved through the regulation of autophagy by targeting ATG12. (PMID:30027574)
• CRL4(AMBRA)(1) modulates interleukin-6/STAT3 signaling and HIV-1 infectivity that are regulated by CRL5(SOCS)(3) and CRL5(VIF), respectively. Thus, by discovering a substrate of CRL4(AMBRA)(1), ELOC, the shared adapter of CRL5 ubiquitin ligases, we uncovered a novel CRL cross-regulation pathway. (PMID:30166453)
• AMBRA1 regulates mitophagy through a novel pathway, in which HUWE1 and IKKalpha are key factors, shedding new lights on the regulation of mitochondrial quality control and homoeostasis in mammalian cells. (PMID:30217973)
• AMBRA1 is a key modulator of T cell differentiation. Through its ability to interact with the phosphatase PP2A, AMBRA1 promotes the FOXO3 stability. (PMID:30513302)
• Epidermal autophagy and beclin 1 regulator 1 and loricrin: a paradigm shift in the prognostication and stratification of the American Joint Committee on Cancer stage I melanomas. (PMID:31056744)
• HUWE1 controls MCL1 stability to unleash AMBRA1-induced mitophagy. (PMID:31434979)
• Rare mutations in the autophagy-regulating gene AMBRA1 contribute to human neural tube defects. (PMID:32333458)
• The autophagy protein Ambra1 regulates gene expression by supporting novel transcriptional complexes. (PMID:32616651)
• HPV sensitizes OPSCC cells to cisplatin-induced apoptosis by inhibiting autophagy through E7-mediated degradation of AMBRA1. (PMID:33172332)
• The Role of Cardiolipin as a Scaffold Mitochondrial Phospholipid in Autophagosome Formation: In Vitro Evidence. (PMID:33562550)
• AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity. (PMID:33854232)
• CRL4(AMBRA1) is a master regulator of D-type cyclins. (PMID:33854235)
• The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D. (PMID:33854239)
• Loss of Ambra1 promotes melanoma growth and invasion. (PMID:33953176)
• Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling. (PMID:34302498)
• AMBRA1 Promotes TGFbeta Signaling via Nonproteolytic Polyubiquitylation of Smad4. (PMID:34362797)
• The Long-Lost Ligase: CRL4(AMBRA1) Regulates the Stability of D-Type Cyclins. (PMID:34495753)
• AMBRA1 Negatively Regulates the Function of ALDH1B1, a Cancer Stem Cell Marker, by Controlling Its Ubiquitination. (PMID:34769507)
• AMBRA1 regulates mitophagy by interacting with ATAD3A and promoting PINK1 stability. (PMID:34798798)
• [Homocysteine promotes human hepatocyte autophagy through activating the activating molecule in beclin-1-regulated autophage (AMBRA1)]. (PMID:36082712)
• The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma. (PMID:36243772)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ambra1a	ENSDARG00000008322
danio_rerio	ambra1b	ENSDARG00000039878
mus_musculus	Ambra1	ENSMUSG00000040506
rattus_norvegicus	Ambra1	ENSRNOG00000017422

Protein

Protein identifiers

Activating molecule in BECN1-regulated autophagy protein 1 — Q9C0C7 (reviewed: Q9C0C7)

Alternative names: DDB1- and CUL4-associated factor 3

All UniProt accessions (4): Q9C0C7, A0A075B6T1, E9PL55, H0YE34

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-recognition component of a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex involved in cell cycle control and autophagy. The DCX(AMBRA1) complex specifically mediates the polyubiquitination of target proteins such as BECN1, CCND1, CCND2, CCND3, ELOC and ULK1. Acts as an upstream master regulator of the transition from G1 to S cell phase: AMBRA1 specifically recognizes and binds phosphorylated cyclin-D (CCND1, CCND2 and CCND3), leading to cyclin-D ubiquitination by the DCX(AMBRA1) complex and subsequent degradation. By controlling the transition from G1 to S phase and cyclin-D degradation, AMBRA1 acts as a tumor suppressor that promotes genomic integrity during DNA replication and counteracts developmental abnormalities and tumor growth. AMBRA1 also regulates the cell cycle by promoting MYC dephosphorylation and degradation independently of the DCX(AMBRA1) complex: acts via interaction with the catalytic subunit of protein phosphatase 2A (PPP2CA), which enhances interaction between PPP2CA and MYC, leading to MYC dephosphorylation and degradation. Acts as a regulator of Cul5-RING (CRL5) E3 ubiquitin-protein ligase complexes by mediating ubiquitination and degradation of Elongin-C (ELOC) component of CRL5 complexes. Acts as a key regulator of autophagy by modulating the BECN1-PIK3C3 complex: controls protein turnover during neuronal development, and regulates normal cell survival and proliferation. In normal conditions, AMBRA1 is tethered to the cytoskeleton via interaction with dyneins DYNLL1 and DYNLL2. Upon autophagy induction, AMBRA1 is released from the cytoskeletal docking site to induce autophagosome nucleation by mediating ubiquitination of proteins involved in autophagy. The DCX(AMBRA1) complex mediates ‘Lys-63’-linked ubiquitination of BECN1, increasing the association between BECN1 and PIK3C3 to promote PIK3C3 activity. In collaboration with TRAF6, AMBRA1 mediates ‘Lys-63’-linked ubiquitination of ULK1 following autophagy induction, promoting ULK1 stability and kinase activity. Also activates ULK1 via interaction with TRIM32: TRIM32 stimulates ULK1 through unanchored ‘Lys-63’-linked polyubiquitin chains. Also acts as an activator of mitophagy via interaction with PRKN and LC3 proteins (MAP1LC3A, MAP1LC3B or MAP1LC3C); possibly by bringing damaged mitochondria onto autophagosomes. Also activates mitophagy by acting as a cofactor for HUWE1; acts by promoting HUWE1-mediated ubiquitination of MFN2. AMBRA1 is also involved in regulatory T-cells (Treg) differentiation by promoting FOXO3 dephosphorylation independently of the DCX(AMBRA1) complex: acts via interaction with PPP2CA, which enhances interaction between PPP2CA and FOXO3, leading to FOXO3 dephosphorylation and stabilization. May act as a regulator of intracellular trafficking, regulating the localization of active PTK2/FAK and SRC. Also involved in transcription regulation by acting as a scaffold for protein complexes at chromatin.

Subunit / interactions. Component of the DCX(AMBRA1) E3 ubiquitin ligase complex, also named CRL4(AMBRA1), at least composed of CUL4 (CUL4A or CUL4B), DDB1, AMBRA1 and RBX1. Interacts with BECN1. Probably forms a complex with BECN1 and PIK3C3. Interacts with BECN2. Interacts with BCL2; leading to prevent interaction with BCN1 and autophagy, interaction is disrupted upon autophagy induction. Interacts with ULK1. Interacts (via PxP motifs) with PPP2CA; enhancing interaction between PPP2CA and MYC or FOXO3. Forms a complex with PPP2CA and BECN1; AMBRA1 and BECN1 components of the complex regulate MYC stability via different pathways. Interacts (TQT motifs) with DYNLL1 and DYNLL2; tethering AMBRA1 and the BECN1-PIK3C3 complex in absence of autophagy. Interacts with TRAF6; interaction is required to mediate ‘Lys-63’-linked ubiquitination of ULK1. Interacts with TRIM32; promoting activation of ULK1 by TRIM32 via unanchored ‘Lys-63’-linked polyubiquitin chains. Interacts with PRKN. Interacts (via LIR motif) with LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C). Interacts with HUWE1. Interacts with PTK2/FAK. Interacts with SRC; required for SRC trafficking to autophagosomes.

Subcellular location. Endoplasmic reticulum. Cytoplasm. Cytoskeleton. Cytoplasmic vesicle. Autophagosome. Mitochondrion. Cytosol. Nucleus. Cell junction. Focal adhesion.

Post-translational modifications. Phosphorylation at Ser-52 by MTOR inhibits its ability to regulate autophagy and mediate ubiquitination of ULK1. Phosphorylation by ULK1 in response to autophagy induction abolishes interaction with DYNLL1 and DYNLL2, releasing AMBRA1 from the cytoskeletal docking site to induce autophagosome nucleation. Phosphorylation by MTOR inhibits interaction with PPP2CA and subsequent dephosphorylation of MYC. Phosphorylation at Ser-1043 by CHUK/IKKA promotes its interaction with ATG8 family proteins GABARAP and MAP1LC3B and its mitophagic activity. Ubiquitinated by RNF2 via ‘Lys-48’-linkage in unstressed cells, leading to its degradation by the proteasome. Induction of autophagy promotes stabilization via interaction with CUL4 (CUL4A or CUL4B) and DDB1. Upon prolonged starvation, ubiquitinated and degraded, terminating the autophagy response. Undergoes proteolytic processing by caspase-6 (CASP6), caspase-7 (CASP7) and caspase-8 (CASP8) during apoptosis, resulting in the dismantling of the autophagic machinery and the accomplishment of the programmed cell death program. Also cleaved by calpains during apoptosis, which mediate a complete proteolytic degradation.

Domain organisation. The PxP motifs mediate interaction with the catalytic subunit of protein phosphatase 2A (PPP2CA). The TQT motifs mediate interaction with the dynein light chain proteins DYNLL1 and DYNLL2, tethering AMBRA1 to the cytoskeleton in absence of autophagy. The LIR motif (LC3-interacting region) is required for the interaction with the ATG8 family proteins GABARAP and MAP1LC3B.

Induction. Negatively regulated by microRNA 7-3HG (miR7-3HG), which targets the 3’ untranslated (3’-UTR) region of AMBRA1 transcripts, leading to a decrease of AMBRA1 mRNA and protein levels, thereby inhibiting autophagy. Strongly up-regulated during egulatory T-cells (Treg) differentiation.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the WD repeat AMBRA1 family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q9C0C7-1	1	yes
Q9C0C7-2	2
Q9C0C7-3	3
Q9C0C7-4	4
Q9C0C7-5	5
Q9C0C7-6	6

RefSeq proteins (9): NP_001254711, NP_001254712, NP_001287660, NP_001354397, NP_001354398, NP_001354399, NP_001354400, NP_001373940, NP_060219 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR019775	WD40_repeat_CS	Conserved_site
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily
IPR052596	AMBRA1_autophagy	Family

Pfam: PF00400

UniProt features (113 total): strand 30, mutagenesis site 17, compositionally biased region 12, region of interest 11, modified residue 9, splice variant 6, sequence conflict 6, short sequence motif 5, sequence variant 5, helix 4, repeat 3, turn 2, chain 1, site 1, cross-link 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
8WQR	ELECTRON MICROSCOPY	3.08
9IVD	ELECTRON MICROSCOPY	3.55

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C0C7-F1	49.27	0.17

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 482–483 (cleavage; by caspase-6, caspase-7 and caspase-8)

Post-translational modifications (10): 52, 328, 394, 443, 635, 639, 747, 1043, 1205, 45

Mutagenesis-validated functional residues (17):

Position	Phenotype
1–43	abolished interaction with ddb1.
1–22	abolished interaction with ddb1.
52	impaired phosphorylation by mtor, leading to strong induction of autophagy. does not affect interaction with ddb1.
52	phospho-mimetic mutant; abolished ability to promote autophagy. does not affect interaction with ddb1.
275–277	abolished interaction with ppp2ca and myc, leading to decreased myc dephosphorylation; when associated with 1206-a–a-12
482	abolished cleavage by caspases without affecting cleavage by calpains.
620	abolished interaction with traf6.
642	does not affect interaction with traf6.
682	abolished interaction with traf6.
918	does not affect interaction with traf6.
1043	abolished phosphorylation by chuk/ikka, leading to impaired interaction with atg8 family proteins and reduced mitophagic
1043	phospho-mimetic mutant; increased interaction with atg8 family proteins and increased mitophagic activity.
1049–1052	abolished interaction with lc3 (map1lc3a, map1lc3b or map1lc3c).
1105	in tat1 mutant; abolished interaction with dynll1 and dynll2, leading to constitutive induction of autophagy.
1117	in tat2 mutant; abolished interaction with dynll1 and dynll2, leading to constitutive induction of autophagy.
1134	does not affect interaction with traf6.
1206–1208	abolished interaction with ppp2ca and myc, leading to decreased myc dephosphorylation; when associated with 275-a–a-277

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1632852	Macroautophagy
R-HSA-9612973	Autophagy

MSigDB gene sets: 254 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_NEGATIVE_REGULATION_OF_NEURON_APOPTOTIC_PROCESS, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, GOBP_VACUOLE_ORGANIZATION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, GOBP_NEURAL_TUBE_DEVELOPMENT

GO Biological Process (23): autophagosome assembly (GO:0000045), protein polyubiquitination (GO:0000209), mitophagy (GO:0000423), regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of cell population proliferation (GO:0008285), cellular response to starvation (GO:0009267), positive regulation of autophagy (GO:0010508), negative regulation of cardiac muscle cell apoptotic process (GO:0010667), neural tube development (GO:0021915), cell differentiation (GO:0030154), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), negative regulation of neuron apoptotic process (GO:0043524), positive regulation of regulatory T cell differentiation (GO:0045591), positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (GO:0051897), response to mitochondrial depolarisation (GO:0098780), positive regulation of mitophagy (GO:1901526), positive regulation of free ubiquitin chain polymerization (GO:1904544), regulation of G1/S transition of mitotic cell cycle (GO:2000045), G1/S transition of mitotic cell cycle (GO:0000082), autophagy (GO:0006914), nervous system development (GO:0007399), protein ubiquitination (GO:0016567), response to nutrient levels (GO:0031667)

GO Molecular Function (6): protein phosphatase binding (GO:0019903), ubiquitin protein ligase binding (GO:0031625), GTPase binding (GO:0051020), protein phosphatase activator activity (GO:0072542), ubiquitin-like ligase-substrate adaptor activity (GO:1990756), protein binding (GO:0005515)

GO Cellular Component (15): nucleus (GO:0005634), cytoplasm (GO:0005737), mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), autophagosome (GO:0005776), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), cytoskeleton (GO:0005856), focal adhesion (GO:0005925), axoneme (GO:0005930), phagocytic vesicle (GO:0045335), perinuclear region of cytoplasm (GO:0048471), Cul4-RING E3 ubiquitin ligase complex (GO:0080008), cytoplasmic vesicle (GO:0031410), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Autophagy	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	5
cellular anatomical structure	4
intracellular membrane-bounded organelle	3
cellular response to stress	2
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
protein ubiquitination	1
autophagy of mitochondrion	1
macroautophagy	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cell population proliferation	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
cellular response to nutrient levels	1
response to starvation	1
autophagy	1
positive regulation of catabolic process	1
regulation of autophagy	1
cardiac muscle cell apoptotic process	1
negative regulation of striated muscle cell apoptotic process	1
regulation of cardiac muscle cell apoptotic process	1
nervous system development	1
tube development	1
chordate embryonic development	1
epithelium development	1
cellular developmental process	1
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
negative regulation of apoptotic process	1
regulation of neuron apoptotic process	1
neuron apoptotic process	1
regulatory T cell differentiation	1
positive regulation of T cell differentiation	1
regulation of regulatory T cell differentiation	1

Protein interactions and networks

STRING

2927 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
AMBRA1	PIK3C3	Q8NEB9	999
AMBRA1	BECN1	Q14457	999
AMBRA1	ATG14	Q6ZNE5	997
AMBRA1	UVRAG	Q9P2Y5	997
AMBRA1	PIK3R4	Q99570	996
AMBRA1	TRAF6	Q9Y4K3	986
AMBRA1	SH3GLB1	Q9Y371	985
AMBRA1	BCL2	P10415	931
AMBRA1	NRBF2	Q96F24	924
AMBRA1	RUBCN	Q92622	829
AMBRA1	ULK1	O75385	823
AMBRA1	ATG13	O75143	815
AMBRA1	ATG7	O95352	812
AMBRA1	ATG16L1	Q676U5	809
AMBRA1	ATG12	O94817	778

IntAct

147 interactions, top by confidence:

A	B	Type	Score
BECN1	ATG14	psi-mi:“MI:0914”(association)	0.980
ULK1	ATG13	psi-mi:“MI:0914”(association)	0.940
AMBRA1	BECN1	psi-mi:“MI:0915”(physical association)	0.870
BECN1	AMBRA1	psi-mi:“MI:0915”(physical association)	0.870
CUL4B	COPS2	psi-mi:“MI:0914”(association)	0.790
BECN1	ZWINT	psi-mi:“MI:0914”(association)	0.750
COPS6	RHOBTB1	psi-mi:“MI:0914”(association)	0.730
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
AMBRA1	BCL2	psi-mi:“MI:0403”(colocalization)	0.660
BCL2	AMBRA1	psi-mi:“MI:0915”(physical association)	0.660
AMBRA1	BCL2	psi-mi:“MI:0915”(physical association)	0.660
AMBRA1	BCL2	psi-mi:“MI:0914”(association)	0.660
AMBRA1	BCL2	psi-mi:“MI:2364”(proximity)	0.660
BCL2	AMBRA1	psi-mi:“MI:0195”(covalent binding)	0.660
BCL2	AMBRA1	psi-mi:“MI:0403”(colocalization)	0.660
ULK1	AMBRA1	psi-mi:“MI:0915”(physical association)	0.640
AMBRA1	ULK1	psi-mi:“MI:0915”(physical association)	0.640
CUL4A	COPS2	psi-mi:“MI:0914”(association)	0.640
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640

BioGRID (1306): DDB1 (Affinity Capture-Western), CUL4A (Affinity Capture-Western), CUL4B (Affinity Capture-Western), DYNLL1 (Two-hybrid), AMBRA1 (Affinity Capture-Western), AMBRA1 (Affinity Capture-Western), PIK3C3 (Affinity Capture-Western), AMBRA1 (Affinity Capture-Western), GABARAP (Affinity Capture-Western), BECN1 (Affinity Capture-Western), AMBRA1 (Affinity Capture-Western), AMBRA1 (Affinity Capture-MS), AMBRA1 (Affinity Capture-MS), AMBRA1 (Affinity Capture-MS), AMBRA1 (Affinity Capture-MS)

ESM2 similar proteins: A0A482PJF5, A0A482PJY4, A0A482PUS2, A8WWR3, B3M1F2, B3P4M4, B4GZ07, B4HJA7, B4JSL2, B4KCG1, B4M686, B4N8G7, B4PVI7, B4QVV3, E7FAG6, O13826, O22197, O92503, P13810, P23801, P24647, P32511, P32512, P32828, P38239, P38428, P43528, P90859, Q29B72, Q48B61, Q4ZMD6, Q6FS98, Q7T0Q3, Q8B9B2, Q8QME4, Q8RK09, Q8RK12, Q8RSY1, Q8VYC8, Q8XAN6

Diamond homologs: A2AH22, E7FAG6, Q8SRB0, Q9C0C7, Q9LV28, Q9M3B4, X1WHY6, F1LTR1, O24456, P49026, P93340, Q28D01, Q39336, Q5SP67, Q7K0L4, Q8C6G8, Q9C4Z6, Q9H7D7, A1CUD6, A7TLU2, A8IZG4, A8X8C6, B0R0D7, B0XAF3, B4GDM7, B4JW81, B4LJT7, G0SA60, G0SC29, O13046, O13923, O22468, O75717, O76071, O93377, O94527, P0CS38, P0CS39, P0DPA1, P25382

SIGNOR signaling

16 interactions.

A	Effect	B	Mechanism
AMBRA1	“up-regulates activity”	BECN1	binding
DYNLL1	down-regulates	AMBRA1	binding
DYNLL2	down-regulates	AMBRA1	binding
ULK1	up-regulates	AMBRA1	phosphorylation
AMBRA1	“up-regulates activity”	HUWE1	relocalization
AMBRA1	“up-regulates activity”	TRAF6	binding
AMBRA1	“up-regulates activity”	PPP2CB	binding
CDK1	“up-regulates activity”	AMBRA1	phosphorylation
CyclinB/CDK1	“up-regulates activity”	AMBRA1	phosphorylation
CHUK	“up-regulates activity”	AMBRA1	phosphorylation
RNF2	“down-regulates quantity by destabilization”	AMBRA1	ubiquitination
ULK1/Atg13/Fip200	“up-regulates activity”	AMBRA1	phosphorylation
MTOR	“down-regulates activity”	AMBRA1	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 151 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
DNA Damage Recognition in GG-NER	8	24.0×	4e-07
Inactivation of CSF3 (G-CSF) signaling	5	23.1×	3e-04
Formation of TC-NER Pre-Incision Complex	8	17.8×	3e-06
Neddylation	22	11.0×	2e-14
Macroautophagy	9	10.9×	2e-05
Autophagy	6	9.4×	2e-03
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	7	8.6×	1e-03
EML4 and NUDC in mitotic spindle formation	8	7.8×	9e-04

GO biological processes:

GO term	Partners	Fold	FDR
ubiquitin-dependent protein catabolic process via the C-end degron rule pathway	6	51.9×	3e-07
protein neddylation	5	27.0×	2e-04
cellular response to amino acid stimulus	6	14.1×	5e-04
mitophagy	5	12.2×	4e-03
cellular response to UV	5	11.4×	6e-03
G1/S transition of mitotic cell cycle	7	10.8×	5e-04
autophagosome assembly	6	10.4×	2e-03
protein ubiquitination	27	8.6×	6e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	158
Likely benign	10
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

4164 predictions. Top by Δscore:

Variant	Effect	Δscore
11:46408508:CCTAC:C	donor_loss	1.0000
11:46408509:CTACC:C	donor_loss	1.0000
11:46408510:TAC:T	donor_loss	1.0000
11:46408511:ACC:A	donor_loss	1.0000
11:46408512:C:CA	donor_loss	1.0000
11:46408555:C:A	donor_gain	1.0000
11:46408702:TGGTT:T	acceptor_gain	1.0000
11:46408704:GTT:G	acceptor_gain	1.0000
11:46408705:TT:T	acceptor_gain	1.0000
11:46408707:C:CC	acceptor_gain	1.0000
11:46410265:C:A	donor_gain	1.0000
11:46417911:A:AC	donor_gain	1.0000
11:46417912:C:CT	donor_gain	1.0000
11:46417912:CT:C	donor_gain	1.0000
11:46434843:CCTT:C	donor_loss	1.0000
11:46434844:CTTA:C	donor_loss	1.0000
11:46434845:TTA:T	donor_loss	1.0000
11:46434846:T:TG	donor_loss	1.0000
11:46434847:A:AC	donor_gain	1.0000
11:46434848:C:CC	donor_gain	1.0000
11:46434848:C:CT	donor_loss	1.0000
11:46435033:GGAAG:G	acceptor_gain	1.0000
11:46435034:GAAG:G	acceptor_gain	1.0000
11:46435035:AAG:A	acceptor_gain	1.0000
11:46435036:AG:A	acceptor_gain	1.0000
11:46435038:C:CC	acceptor_gain	1.0000
11:46435038:C:T	acceptor_loss	1.0000
11:46435039:T:C	acceptor_loss	1.0000
11:46435041:C:CT	acceptor_gain	1.0000
11:46435044:C:CT	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000038380 (11:46563382 G>A,C), RS1000045631 (11:46490771 C>T), RS1000051440 (11:46417193 A>T), RS1000053473 (11:46450548 TCCC>T), RS1000057215 (11:46588331 C>CA), RS1000079814 (11:46486811 C>A), RS1000087246 (11:46402713 T>C), RS1000099820 (11:46470359 C>T), RS1000115707 (11:46545223 G>A), RS1000122731 (11:46550024 G>A), RS1000146471 (11:46424566 G>A,C,T), RS1000169757 (11:46580266 T>C), RS1000181815 (11:46430207 G>C), RS1000192247 (11:46410623 G>A), RS1000204113 (11:46451702 C>CT)

Disease associations

OMIM: gene MIM:611359 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
neural tube defects, susceptibility to	Strong	Autosomal dominant

Mondo (4): esophageal atresia (MONDO:0001044), pyloric stenosis (MONDO:0001561), neural tube defect (MONDO:0018075), neural tube defects, susceptibility to (MONDO:0020705)

Orphanet (2): Neural tube defect (Orphanet:3388), Spina bifida and other spinal dysraphisms (Orphanet:823)

HPO phenotypes

2 total (2 of 2 shown, HPO-id order):

HPO	Term
HP:0002032	Esophageal atresia
HP:0002021	Pyloric stenosis

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST000763_2	Immunoglobulin A	2.000000e-06
GCST003814_31	Selective IgA deficiency	7.000000e-10
GCST004521_122	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_165	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST004946_84	Schizophrenia	7.000000e-12
GCST006803_20	Schizophrenia	3.000000e-13
GCST007201_118	Schizophrenia	2.000000e-11
GCST007201_239	Schizophrenia	3.000000e-10
GCST007449_2	Normal facial asymmetry (angle of deformation score)	2.000000e-07
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16
GCST008158_39	Body mass index	3.000000e-07
GCST008595_150	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	8.000000e-10
GCST009600_131	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	1.000000e-08
GCST009863_13	Insulin-related traits (multivariate analysis)	2.000000e-17
GCST012100_20	Hypertrophic cardiomyopathy (sarcomere positive)	1.000000e-16

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004747	protein measurement
EFO:0009751	facial asymmetry measurement
EFO:0004340	body mass index
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0004467	insulin measurement

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D004933	Esophageal Atresia	C06.198.330; C06.405.117.260; C16.131.314.330
D017219	Gastric Outlet Obstruction	C06.405.748.340
D009436	Neural Tube Defects	C10.500.680; C16.131.666.680
D011707	Pyloric Stenosis	C06.405.748.340.690

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation	2
Cisplatin	increases expression, decreases response to substance	2
Formaldehyde	decreases expression, increases expression	2
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
bisphenol A	decreases methylation	1
beta-lapachone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
buprofezin	increases expression	1
abrine	increases expression	1
(+)-JQ1 compound	increases expression	1
Arsenic	affects methylation	1
Carbonyl Cyanide m-Chlorophenyl Hydrazone	affects binding, increases reaction	1
Endosulfan	decreases expression	1
Gallic Acid	increases expression	1
Promethazine	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Vitamin E	increases expression	1
Asbestos, Serpentine	decreases methylation	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00556283	PHASE4	COMPLETED	RCT: STARR vs Biofeedback
NCT00301587	PHASE3	WITHDRAWN	A Study to Evaluate Folate Levels in Women Taking Oral Contraceptives
NCT00468481	PHASE3	COMPLETED	Efficacy and Safety Study for an Oral Contraceptive Containing Folate
NCT00226044	PHASE3	COMPLETED	Rectal and Oral Omeprazole Treatment of Reflux Disease in Infants.
NCT01392989	PHASE2	COMPLETED	Post T-plant Infusion of Allogeneic Cytokine Induced Killer (CIK) Cells as Consolidative Therapy in Myelodysplastic Syndromes/Myeloproliferative Disorders
NCT03127345	PHASE2	WITHDRAWN	Omega 3 Fatty Acid Treatment for Pediatric Musculoskeletal Health
NCT00452829	PHASE1	COMPLETED	Prevention of Neural Tube Defects by Inositol in Conjunction With Folic Acid (PONTI Study)
NCT03794011	PHASE1	ACTIVE_NOT_RECRUITING	Patch vs. No Patch Fetoscopic Meningomyelocele Repair Study
NCT02230072	PHASE1	COMPLETED	Fetoscopic Meningomyelocele Repair Study
NCT00341068	Not specified	TERMINATED	Genetic Analysis of Neural Tube and Orofacial Cleft Defects in the Irish Population
NCT00394862	Not specified	COMPLETED	Efficacy of Weekly Versus Daily Folic Acid Supplementation
NCT01244399	Not specified	COMPLETED	Influence of Espresso on Adsorption of Myo-inositol
NCT01253746	Not specified	UNKNOWN	Genetics of Neural Tube Defects
NCT01743196	Not specified	COMPLETED	Folate Metabolism in Normal Weight and Obese Women of Child-bearing Age
NCT03090633	Not specified	ACTIVE_NOT_RECRUITING	Fetoscopic Repair of Isolated Fetal Spina Bifida
NCT03315637	Not specified	UNKNOWN	Fetal Endoscopic Surgery for Spina Bifida
NCT03856034	Not specified	RECRUITING	Laparotomy Versus Percutaneous Endoscopic Correction of Myelomeningocele
NCT03936322	Not specified	COMPLETED	Minimally Invasive Fetoscopic Regenerative Repair of Spina Bifida - A Pilot Study
NCT04135274	Not specified	COMPLETED	Is Neutrophil to Lymphocyte Ratio a Prognostic Factor of Sepsis in Newborns With Operated Neural Tube Defects?
NCT04140669	Not specified	TERMINATED	Automated Myocardial Performance Index Using Samsung HERA W10
NCT04362592	Not specified	ACTIVE_NOT_RECRUITING	In-Utero Endoscopic Correction of Spina Bifida
NCT04523233	Not specified	UNKNOWN	Metals/Vitamins Levels in NTD
NCT04760509	Not specified	UNKNOWN	Short- Term Follow up Of Neonates Born With Neural Tube Defect
NCT04770805	Not specified	ACTIVE_NOT_RECRUITING	In Utero Fetoscopic Repair Program for Sacral Myelomeningoceles and Mye-LDM
NCT05454085	Not specified	COMPLETED	Could Bisphenol-A Have a Role in the Etiology of Neural Tube Defects
NCT05672849	Not specified	RECRUITING	Safety and Efficacy of Devices Used in Fetoscopic Neural Tube Defect Repair Cases
NCT05883761	Not specified	COMPLETED	Birth Outcomes In Eswatini After Transition To Dolutegravir-Based Treatment
NCT05935631	Not specified	COMPLETED	Feasibility, Acceptability and Directional Signal Effect on Blood Folate Levels of Iodized Salt Fortified With Folic Acid: Clinical Study
NCT06135883	Not specified	COMPLETED	Assessing Folic Acid in High-Risk Pregnancy for Neural Tube Defects
NCT06174883	Not specified	COMPLETED	Salt-FA to Increase Folate Levels
NCT06734611	Not specified	NOT_YET_RECRUITING	Folic Acid Salt Study (FISFA Zambia)
NCT06904612	Not specified	COMPLETED	Using Iodized Salt to Improve Serum Folate, B12 and Iron Levels
NCT06946563	Not specified	RECRUITING	Fetoscopic Neural Tube Defect Repair
NCT02033772	Not specified	COMPLETED	Prospective Data Collection of Patients < 6 Months of Age Undergoing Thoracoscopic Surgery
NCT02466451	Not specified	COMPLETED	Study in Children With the Diagnosis of Congenital Diaphragmatic Hernia (CDH) and Oesophageal Atresia (EA)
NCT02525705	Not specified	COMPLETED	Dumping Syndrome After Operation of Esophageal Atresia Type III
NCT02883725	Not specified	COMPLETED	National Register of Oesophageal Atresia
NCT03023865	Not specified	UNKNOWN	Individualized Management for Long Gap Esophageal Atresia
NCT03415893	Not specified	COMPLETED	High-resolution Esophageal Manometry
NCT03455881	Not specified	UNKNOWN	Phenotypic and Genetic Assessment of Tracheal and Esophageal Birth Defects in Patients