FABP9

Summary

FABP9 (fatty acid binding protein 9, HGNC:3563) is a protein-coding gene on chromosome 8q21.13, encoding Fatty acid-binding protein 9 (Q0Z7S8).

Predicted to enable long-chain fatty acid binding activity. Predicted to be involved in long-chain fatty acid transport. Predicted to be located in cytoplasm. Predicted to be active in cytosol and nucleus.

Source: NCBI Gene 646480 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 24 total
• Druggable target: yes
• MANE Select transcript: NM_001080526

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3563
Approved symbol	FABP9
Name	fatty acid binding protein 9
Location	8q21.13
Locus type	gene with protein product
Status	Approved
Aliases	PERF, T-FABP, PERF15
Ensembl gene	ENSG00000205186
Ensembl biotype	protein_coding
OMIM	620856
Entrez	646480

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000379071

RefSeq mRNA: 1 — MANE Select: NM_001080526 NM_001080526

Canonical transcript exons

ENST00000379071 — 4 exons

Exon	Start	End
ENSE00001479674	81458253	81458433
ENSE00001479676	81458602	81458703
ENSE00001479677	81459165	81459337
ENSE00001479679	81461451	81461579

Expression profiles

Bgee: expression breadth broad, 50 present calls, max score 56.03.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0739 / max 96.5778, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93752	0.0739	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
subcutaneous adipose tissue	UBERON:0002190	56.03	gold quality
adipose tissue	UBERON:0001013	55.43	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	55.19	gold quality
omental fat pad	UBERON:0010414	54.66	gold quality
thoracic mammary gland	UBERON:0005200	46.47	gold quality
skin of abdomen	UBERON:0001416	43.83	gold quality
zone of skin	UBERON:0000014	42.93	gold quality
skin of leg	UBERON:0001511	42.50	gold quality
granulocyte	CL:0000094	40.71	gold quality
heart left ventricle	UBERON:0002084	39.79	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
skeletal muscle tissue	UBERON:0001134	36.97	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle of leg	UBERON:0001383	35.21	gold quality
gastrocnemius	UBERON:0001388	35.13	gold quality
heart	UBERON:0000948	35.07	gold quality
muscle tissue	UBERON:0002385	33.70	gold quality
right testis	UBERON:0004534	32.52	silver quality
left testis	UBERON:0004533	32.26	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
testis	UBERON:0000473	31.96	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
placenta	UBERON:0001987	31.41	silver quality
left uterine tube	UBERON:0001303	31.26	gold quality
tibial nerve	UBERON:0001323	31.23	gold quality
left coronary artery	UBERON:0001626	31.13	gold quality
sural nerve	UBERON:0015488	30.93	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.13

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Serum A-FABP might be a prognostic marker of body weight loss suggesting a preventive therapeutic intervention. (PMID:18803274)
• FABP9 is a valuable prognostic marker to predict the outcomes of prostate cancer patients, perhaps by playing an important role in prostate cancer cell invasion. (PMID:27779102)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	fabp4b	ENSDARG00000002311
danio_rerio	fabp4a	ENSDARG00000017299
danio_rerio	rbp7a	ENSDARG00000091906
danio_rerio	rbp5	ENSDARG00000101481
danio_rerio		ENSDARG00000109259
mus_musculus	Fabp9	ENSMUSG00000027528
rattus_norvegicus	Fabp9	ENSRNOG00000011082
drosophila_melanogaster	fabp	FBGN0037913
caenorhabditis_elegans		WBGENE00002259
caenorhabditis_elegans		WBGENE00002260

Paralogs (15): RBP2 (ENSG00000114113), RBP1 (ENSG00000114115), FABP3 (ENSG00000121769), RBP5 (ENSG00000139194), CRABP2 (ENSG00000143320), FABP2 (ENSG00000145384), PMP2 (ENSG00000147588), RBP7 (ENSG00000162444), FABP1 (ENSG00000163586), FABP7 (ENSG00000164434), FABP5 (ENSG00000164687), CRABP1 (ENSG00000166426), FABP6 (ENSG00000170231), FABP4 (ENSG00000170323), FABP12 (ENSG00000197416)

Protein

Protein identifiers

Fatty acid-binding protein 9 — Q0Z7S8 (reviewed: Q0Z7S8)

Alternative names: Testis lipid-binding protein, Testis-type fatty acid-binding protein

All UniProt accessions (1): Q0Z7S8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

Similarity. Belongs to the calycin superfamily. Fatty-acid binding protein (FABP) family.

RefSeq proteins (1): NP_001073995* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000463	Fatty_acid-bd	Domain
IPR000566	Lipocln_cytosolic_FA-bd_dom	Domain
IPR012674	Calycin	Homologous_superfamily
IPR031259	ILBP	Family

Pfam: PF00061

UniProt features (18 total): strand 10, modified residue 4, helix 3, chain 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
4A60	X-RAY DIFFRACTION	1.53
7FY1	X-RAY DIFFRACTION	2.01

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q0Z7S8-F1	96.73	0.95

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 (4): 13, 14, 44, 91

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-163560	Triglyceride catabolism

MSigDB gene sets: 41 (showing top): REACTOME_TRIGLYCERIDE_CATABOLISM, GOBP_ORGANIC_ACID_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, GOBP_MONOCARBOXYLIC_ACID_TRANSPORT, AFFAR_YY1_TARGETS_DN, GOBP_LONG_CHAIN_FATTY_ACID_TRANSPORT, GOBP_LIPID_LOCALIZATION, GOBP_FATTY_ACID_TRANSPORT, GOMF_LONG_CHAIN_FATTY_ACID_BINDING, GOMF_FATTY_ACID_BINDING, GOMF_ORGANIC_ACID_BINDING, GOMF_LIPID_BINDING, chr8q21, GOMF_MONOCARBOXYLIC_ACID_BINDING

GO Biological Process (1): long-chain fatty acid transport (GO:0015909)

GO Molecular Function (2): long-chain fatty acid binding (GO:0036041), lipid binding (GO:0008289)

GO Cellular Component (3): nucleus (GO:0005634), cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Triglyceride metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
fatty acid transport	1
fatty acid binding	1
binding	1
intracellular membrane-bounded organelle	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

424 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FABP9	FABP6	P51161	667
FABP9	GOT2	P00505	509
FABP9	FABP1	P07148	472
FABP9	RESP18	Q5W5W9	413
FABP9	MOGAT3	Q86VF5	403
FABP9	DDX4	Q9NQI0	392
FABP9	WBP2NL	Q6ICG8	389
FABP9	SORD	Q00796	380
FABP9	SYCP3	Q8IZU3	372
FABP9	TXN	P10599	366
FABP9	TEX101	Q9BY14	360
FABP9	DMRT1	Q9Y5R6	360
FABP9	LCN9	Q8WX39	354
FABP9	YBX2	Q9Y2T7	353
FABP9	CXCL16	Q9H2A7	353
FABP9	ACRV1	P26436	353

IntAct

0 interactions, top by confidence:

BioGRID (1): ODF2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0K0MJ13, A0A0K0MJN3, A6YLM6, C4N147, O01812, O01814, O02772, O08716, O13008, O15540, O45035, O97788, P02689, P02690, P02691, P04117, P05413, P06768, P07483, P0C6G6, P10790, P11404, P15090, P24526, P29498, P41496, P41509, P48035, P50120, P50121, P51880, P55051, P55052, P55053, P70623, P80049, P86412, Q01469, Q02970, Q05423

Diamond homologs: A0A0K0MJ13, A0A0K0MJN3, A6NFH5, A6YLM6, A8MUU1, B7SUM8, C4N147, O01812, O01814, O02323, O02324, O02772, O08716, O13008, O15540, O42386, O45035, O76821, O97788, P02689, P02690, P02691, P02694, P02696, P04117, P05413, P06768, P07148, P07483, P09455, P0C6G6, P10790, P11404, P12710, P15090, P22935, P24526, P29373, P29498, P29762

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	1
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

353 predictions. Top by Δscore:

Variant	Effect	Δscore
8:81458702:CT:C	acceptor_gain	1.0000
8:81458704:C:CC	acceptor_gain	1.0000
8:81459173:T:A	donor_gain	1.0000
8:81458429:CATTC:C	acceptor_gain	0.9900
8:81458434:C:A	acceptor_loss	0.9900
8:81458434:C:CC	acceptor_gain	0.9900
8:81458700:TGCT:T	acceptor_gain	0.9900
8:81458704:C:CG	acceptor_loss	0.9900
8:81458705:T:G	acceptor_loss	0.9900
8:81458710:A:C	acceptor_gain	0.9900
8:81458713:C:CT	acceptor_gain	0.9900
8:81459160:CTGA:C	donor_loss	0.9900
8:81459163:A:C	donor_loss	0.9900
8:81459164:C:G	donor_loss	0.9900
8:81459335:CTC:C	acceptor_gain	0.9900
8:81459669:AGAG:A	donor_gain	0.9900
8:81461446:CTCAC:C	donor_loss	0.9900
8:81461447:TCA:T	donor_loss	0.9900
8:81461448:CA:C	donor_loss	0.9900
8:81461449:A:AC	donor_gain	0.9900
8:81461449:AC:A	donor_gain	0.9900
8:81461449:ACCCA:A	donor_loss	0.9900
8:81461450:C:CA	donor_loss	0.9900
8:81461450:C:CC	donor_gain	0.9900
8:81461450:CC:C	donor_gain	0.9900
8:81458431:TTC:T	acceptor_gain	0.9800
8:81458595:AACTT:A	donor_loss	0.9800
8:81458596:ACT:A	donor_loss	0.9800
8:81458597:CT:C	donor_loss	0.9800
8:81458598:TTA:T	donor_loss	0.9800

AlphaMissense

888 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:81458701:G:C	S83R	0.959
8:81458701:G:T	S83R	0.959
8:81458703:T:G	S83R	0.959
8:81459175:C:G	R79P	0.956
8:81458407:G:C	S125R	0.947
8:81458407:G:T	S125R	0.947
8:81458409:T:G	S125R	0.947
8:81459198:A:C	F71L	0.940
8:81459198:A:T	F71L	0.940
8:81459200:A:G	F71L	0.940
8:81459216:G:C	F65L	0.927
8:81459216:G:T	F65L	0.927
8:81459218:A:G	F65L	0.927
8:81458629:T:A	R107S	0.924
8:81458629:T:G	R107S	0.924
8:81461497:C:A	W9C	0.907
8:81461497:C:G	W9C	0.907
8:81461499:A:G	W9R	0.905
8:81461499:A:T	W9R	0.905
8:81461473:A:C	F17L	0.902
8:81461473:A:T	F17L	0.902
8:81461475:A:G	F17L	0.902
8:81458696:A:T	I85K	0.898
8:81458609:A:G	M114T	0.878
8:81458662:T:A	Q96H	0.866
8:81458662:T:G	Q96H	0.866
8:81459319:C:G	R31P	0.846
8:81458658:A:G	W98R	0.845
8:81458658:A:T	W98R	0.845
8:81458663:T:G	Q96P	0.836

dbSNP variants (sampled 300 via entrez): RS1000133817 (8:81457835 T>G), RS1001467009 (8:81460800 A>G), RS1001967033 (8:81461235 T>A,C), RS1002877881 (8:81458400 T>C), RS1002885395 (8:81459312 C>T), RS1003232349 (8:81462562 T>C), RS1003632971 (8:81462651 A>C), RS1004377611 (8:81462850 C>T), RS1004389216 (8:81463176 A>G), RS1005242830 (8:81459598 G>T), RS1006005379 (8:81461907 G>A), RS1006086220 (8:81463334 A>G), RS1006154503 (8:81457920 G>A), RS1006364171 (8:81461710 A>G), RS1007425920 (8:81458867 C>T)

Disease associations

OMIM: gene MIM:620856 | 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
GCST003542_123	Night sleep phenotypes	7.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3826865 (SINGLE PROTEIN)

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other protein — Fatty acid-binding proteins

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	1
Valproic Acid	decreases methylation	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Permethrin	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3828900	Binding	Displacement of 1,8-ANS from His6-tagged FABP9 (unknown origin) expressed in Escherichia coli BL21(DE3) cells at 25 uM by fluorescence assay relative to control	The discovery of novel and selective fatty acid binding protein 4 inhibitors by virtual screening and biological evaluation. — Bioorg Med Chem

Clinical trials (associated diseases)

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