LDAF1

Summary

LDAF1 (lipid droplet assembly factor 1, HGNC:30136) is a protein-coding gene on chromosome 16p12.3, encoding Lipid droplet assembly factor 1 (Q96B96). Plays an important role in the formation of lipid droplets (LD) which are storage organelles at the center of lipid and energy homeostasis.

Involved in lipid droplet formation. Located in endoplasmic reticulum membrane and lipid droplet.

Source: NCBI Gene 57146 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_001301771

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30136
Approved symbol	LDAF1
Name	lipid droplet assembly factor 1
Location	16p12.3
Locus type	gene with protein product
Status	Approved
Aliases	promethin
Ensembl gene	ENSG00000011638
Ensembl biotype	protein_coding
OMIM	611304
Entrez	57146

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 26 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000233047, ENST00000261388, ENST00000451578, ENST00000572258, ENST00000572599, ENST00000573487, ENST00000573688, ENST00000574092, ENST00000577162, ENST00000910916, ENST00000910917, ENST00000910918, ENST00000910919, ENST00000910920, ENST00000910921, ENST00000910922, ENST00000910923, ENST00000910924, ENST00000910925, ENST00000938563, ENST00000938564, ENST00000938565, ENST00000938566, ENST00000966397, ENST00000966398, ENST00000966399, ENST00000966400, ENST00000966401, ENST00000966402

RefSeq mRNA: 6 — MANE Select: NM_001301771 NM_001301769, NM_001301771, NM_001301773, NM_001301774, NM_001301775, NM_020422

CCDS: CCDS10595, CCDS76841, CCDS76842

Canonical transcript exons

ENST00000233047 — 5 exons

Exon	Start	End
ENSE00000676583	21174010	21174148
ENSE00001523630	21179475	21180616
ENSE00001523631	21161085	21161278
ENSE00002640435	21158674	21158746
ENSE00003478230	21170437	21170605

Expression profiles

Bgee: expression breadth ubiquitous, 141 present calls, max score 96.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.4933 / max 265.9175, expressed in 1801 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
153099	25.0689	1790
153097	1.6842	1052
153098	0.7402	494

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	96.77	gold quality
zone of skin	UBERON:0000014	96.64	gold quality
skin of abdomen	UBERON:0001416	96.46	gold quality
heart left ventricle	UBERON:0002084	96.10	gold quality
apex of heart	UBERON:0002098	96.02	gold quality
right coronary artery	UBERON:0001625	95.53	gold quality
descending thoracic aorta	UBERON:0002345	95.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.47	gold quality
mucosa of stomach	UBERON:0001199	95.41	gold quality
skeletal muscle tissue	UBERON:0001134	95.17	gold quality
popliteal artery	UBERON:0002250	95.10	gold quality
urinary bladder	UBERON:0001255	95.08	gold quality
tibial artery	UBERON:0007610	95.08	gold quality
stromal cell of endometrium	CL:0002255	94.98	gold quality
artery	UBERON:0001637	94.88	gold quality
heart	UBERON:0000948	94.87	gold quality
esophagus mucosa	UBERON:0002469	94.82	gold quality
vagina	UBERON:0000996	94.61	gold quality
lower esophagus mucosa	UBERON:0035834	94.58	gold quality
thoracic aorta	UBERON:0001515	94.38	gold quality
ascending aorta	UBERON:0001496	94.29	gold quality
cortical plate	UBERON:0005343	94.01	gold quality
skeletal muscle organ	UBERON:0014892	93.86	gold quality
muscle tissue	UBERON:0002385	93.85	gold quality
muscle of leg	UBERON:0001383	93.81	gold quality
esophagus	UBERON:0001043	93.51	gold quality
gastrocnemius	UBERON:0001388	93.42	gold quality
ectocervix	UBERON:0012249	93.18	gold quality
right atrium auricular region	UBERON:0006631	93.14	gold quality
left coronary artery	UBERON:0001626	93.09	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	122.15
E-ANND-3	yes	7.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting LDAF1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-101-3P	99.94	75.03	2230
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-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311

Literature-anchored findings (GeneRIF, showing 2)

• promethin is indeed an lipid droplet-associated protein that forms a complex with seipin. (PMID:30901948)
• The LDAF1binds seipin and determines the sites of lipid droplet formation in the ER. LDAF1-seipin complex is the core protein machinery that facilitates LD biogenesis. (PMID:31708432)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ldaf1	ENSMUSG00000030917
rattus_norvegicus	Ldaf1	ENSRNOG00000048250

Protein

Protein identifiers

Lipid droplet assembly factor 1 — Q96B96 (reviewed: Q96B96)

Alternative names: Promethin, Transmembrane protein 159

All UniProt accessions (5): Q96B96, I3L288, I3L319, I3NI21, I3NI23

UniProt curated annotations — full annotation on UniProt →

Function. Plays an important role in the formation of lipid droplets (LD) which are storage organelles at the center of lipid and energy homeostasis. In association with BSCL2/seipin, defines the sites of LD formation in the endoplasmic reticulum.

Subunit / interactions. Interacts with isoform 1 and isoform 3 of BSCL2/seipin to form an oligomeric complex.

Subcellular location. Endoplasmic reticulum membrane. Lipid droplet.

Tissue specificity. Expressed at high levels in the heart and skeletal muscle. Expressed at low levels in kidney, small intestine, lung and liver.

Similarity. Belongs to the LDAF1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96B96-1	1	yes
Q96B96-2	2

RefSeq proteins (6): NP_001288698, NP_001288700, NP_001288702, NP_001288703, NP_001288704, NP_065155 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029709	LDAF1	Family

Pfam: PF16015

UniProt features (14 total): topological domain 5, transmembrane region 4, sequence variant 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96B96-F1	79.31	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 146 (showing top): CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, GOLDRATH_IMMUNE_MEMORY, MISSIAGLIA_REGULATED_BY_METHYLATION_UP, MODULE_205, GOBP_ORGANELLE_ASSEMBLY, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0, MODULE_60, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN, YAGI_AML_WITH_11Q23_REARRANGED, chr16p12, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, XU_CREBBP_TARGETS_UP, GARY_CD5_TARGETS_UP, GOCC_ORGANELLE_SUBCOMPARTMENT, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP

GO Biological Process (1): lipid droplet formation (GO:0140042)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), lipid droplet (GO:0005811), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid storage	1
lipid droplet organization	1
membraneless organelle assembly	1
binding	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
intracellular membraneless organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

286 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LDAF1	BSCL2	Q96G97	851
LDAF1	PPARA	Q07869	674
LDAF1	KCTD9	Q7L273	518
LDAF1	PPARG	P37231	505
LDAF1	CRIM1	Q9NZV1	442
LDAF1	ANGEL1	Q9UNK9	441
LDAF1	FITM2	Q8N6M3	406
LDAF1	C5orf15	Q8NC54	400
LDAF1	CCDC28A	Q8IWP9	400
LDAF1	TMEM256	Q8N2U0	394
LDAF1	DUSP19	Q8WTR2	389
LDAF1	FITM1	A5D6W6	384
LDAF1	BTBD3	Q9Y2F9	384
LDAF1	PRPSAP1	Q14558	382
LDAF1	GPAT3	Q53EU6	379

IntAct

60 interactions, top by confidence:

A	B	Type	Score
GAD2	LDAF1	psi-mi:“MI:0915”(physical association)	0.720
LDAF1	COQ8A	psi-mi:“MI:0915”(physical association)	0.720
COQ8A	LDAF1	psi-mi:“MI:0915”(physical association)	0.720
LDAF1	CACFD1	psi-mi:“MI:0915”(physical association)	0.670
CACFD1	LDAF1	psi-mi:“MI:0915”(physical association)	0.670
FAF2	UBB	psi-mi:“MI:0914”(association)	0.640
USE1	NBAS	psi-mi:“MI:0914”(association)	0.640
LDAF1		psi-mi:“MI:0915”(physical association)	0.560
	LDAF1	psi-mi:“MI:0915”(physical association)	0.560
LDAF1	HYR1	psi-mi:“MI:0915”(physical association)	0.560
S100B	LDAF1	psi-mi:“MI:0915”(physical association)	0.560
LDAF1	TMEM19	psi-mi:“MI:0915”(physical association)	0.560
SLC48A1	LDAF1	psi-mi:“MI:0915”(physical association)	0.560
LDAF1	SEC22A	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (72): TMEM159 (Two-hybrid), TMEM159 (Two-hybrid), TMEM159 (Two-hybrid), ZNF391 (Two-hybrid), TMEM159 (Affinity Capture-MS), TMEM159 (Two-hybrid), TMEM159 (Two-hybrid), TMEM159 (Affinity Capture-MS), TMEM159 (Affinity Capture-MS), TMEM159 (Affinity Capture-MS), TMEM159 (Two-hybrid), TMEM159 (Two-hybrid), TMEM159 (Affinity Capture-MS), SEC22A (Two-hybrid), GAD2 (Two-hybrid)

ESM2 similar proteins: A0A060L102, A0A060L4I9, A0A1I9R3Y6, A2XL05, A6MGW7, C0HM28, C3S7F0, C3S7F1, O04925, P13436, P21641, P29109, P29110, P29111, P29525, P29526, P29527, P29528, P29529, P29530, P29531, Q00650, Q10EK7, Q39165, Q42431, Q42574, Q42980, Q43284, Q43804, Q45W86, Q45W87, Q5F433, Q647G3, Q647G4, Q647G5, Q68F33, Q6GM19, Q6J1J8, Q6UK00, Q84T21

Diamond homologs: Q68F33, Q6GM19, Q6UK00, Q922Z1, Q96B96

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1295 predictions. Top by Δscore:

Variant	Effect	Δscore
16:21161076:T:TA	acceptor_gain	1.0000
16:21170432:TACA:T	acceptor_loss	1.0000
16:21170434:CAGG:C	acceptor_loss	1.0000
16:21170435:A:AG	acceptor_gain	1.0000
16:21170435:A:T	acceptor_loss	1.0000
16:21170435:AGGT:A	acceptor_gain	1.0000
16:21170436:G:GG	acceptor_gain	1.0000
16:21170436:GGT:G	acceptor_gain	1.0000
16:21170436:GGTG:G	acceptor_gain	1.0000
16:21170602:G:GT	donor_gain	1.0000
16:21170603:A:T	donor_gain	1.0000
16:21158743:GCAG:G	donor_gain	0.9900
16:21158744:CAGG:C	donor_loss	0.9900
16:21158745:AGGT:A	donor_loss	0.9900
16:21158747:GTGA:G	donor_loss	0.9900
16:21158748:T:G	donor_loss	0.9900
16:21159266:C:A	donor_gain	0.9900
16:21159337:C:CA	donor_gain	0.9900
16:21161077:G:A	acceptor_gain	0.9900
16:21161083:A:AG	acceptor_gain	0.9900
16:21161084:G:GG	acceptor_gain	0.9900
16:21170428:T:TA	acceptor_gain	0.9900
16:21170435:AG:A	acceptor_gain	0.9900
16:21170435:AGGTG:A	acceptor_gain	0.9900
16:21170436:GG:G	acceptor_gain	0.9900
16:21170436:GGTGG:G	acceptor_gain	0.9900
16:21170559:G:GA	donor_gain	0.9900
16:21170602:GAAGG:G	donor_loss	0.9900
16:21170604:AGGTA:A	donor_loss	0.9900
16:21170605:GG:G	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000094392 (16:21171653 A>C,G), RS1000104829 (16:21165139 T>A), RS1000658086 (16:21169299 A>G), RS1000819565 (16:21175943 C>G), RS1000877952 (16:21156707 A>C,T), RS1001036765 (16:21158647 C>G,T), RS1001316241 (16:21172420 T>A), RS1001455592 (16:21177181 T>C), RS1001549973 (16:21158851 C>T), RS1001621715 (16:21172745 C>A,T), RS1001869580 (16:21158290 G>C), RS1002221488 (16:21171049 TCA>T), RS1002252472 (16:21171217 T>A), RS1002279506 (16:21157870 G>A), RS1002342242 (16:21177636 T>TTG)

Disease associations

OMIM: gene MIM:611304 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, increases expression	5
Valproic Acid	increases expression	3
aristolochic acid I	increases expression	1
testosterone enanthate	affects expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
ICG 001	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Zoledronic Acid	increases expression	1
Leflunomide	decreases expression	1
Copper	increases expression, affects reaction	1
Dexamethasone	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	increases expression	1
Lactic Acid	affects expression	1

Clinical trials (associated diseases)

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