FNDC9

Summary

FNDC9 (fibronectin type III domain containing 9, HGNC:33547) is a protein-coding gene on chromosome 5q33.3, encoding Fibronectin type III domain-containing protein 9 (Q8TBE3).

Predicted to be located in membrane.

Source: NCBI Gene 408263 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_001001343

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33547
Approved symbol	FNDC9
Name	fibronectin type III domain containing 9
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC27121
Ensembl gene	ENSG00000172568
Ensembl biotype	protein_coding
Entrez	408263

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000312349, ENST00000520782

RefSeq mRNA: 1 — MANE Select: NM_001001343 NM_001001343

CCDS: CCDS4337

Canonical transcript exons

ENST00000312349 — 2 exons

Exon	Start	End
ENSE00001211503	157345541	157345677
ENSE00001211510	157341598	157343543

Expression profiles

Bgee: expression breadth broad, 76 present calls, max score 81.49.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.6380 / max 151.6067, expressed in 122 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64517	0.7276	86
64518	0.4753	107
64516	0.3577	39
64519	0.0775	41

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
nucleus accumbens	UBERON:0001882	81.49	gold quality
superior frontal gyrus	UBERON:0002661	81.34	gold quality
hypothalamus	UBERON:0001898	81.29	gold quality
pituitary gland	UBERON:0000007	77.08	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.02	gold quality
cerebellum	UBERON:0002037	76.44	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	76.44	gold quality
cerebellar hemisphere	UBERON:0002245	76.39	gold quality
cerebellar cortex	UBERON:0002129	76.34	gold quality
prefrontal cortex	UBERON:0000451	76.02	gold quality
frontal cortex	UBERON:0001870	75.99	gold quality
primary visual cortex	UBERON:0002436	75.81	gold quality
right frontal lobe	UBERON:0002810	75.23	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.20	gold quality
adenohypophysis	UBERON:0002196	72.36	gold quality
cerebral cortex	UBERON:0000956	71.54	gold quality
brain	UBERON:0000955	71.02	gold quality
anterior cingulate cortex	UBERON:0009835	69.77	gold quality
ventricular zone	UBERON:0003053	65.18	gold quality
caudate nucleus	UBERON:0001873	64.95	gold quality
bone marrow cell	CL:0002092	62.92	silver quality
temporal lobe	UBERON:0001871	62.76	gold quality
amygdala	UBERON:0001876	62.35	gold quality
putamen	UBERON:0001874	62.31	gold quality
bone marrow	UBERON:0002371	58.96	gold quality
islet of Langerhans	UBERON:0000006	58.13	gold quality
Ammon’s horn	UBERON:0001954	52.94	gold quality
colonic epithelium	UBERON:0000397	52.44	gold quality
vermiform appendix	UBERON:0001154	50.05	gold quality
rectum	UBERON:0001052	48.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting FNDC9, 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-126-5P	100.00	72.71	3180
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-4519	99.48	66.10	859
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-642A-3P	99.23	67.67	1258

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fndc9	ENSMUSG00000048721
rattus_norvegicus	Fndc9	ENSRNOG00000073535

Protein

Protein identifiers

Fibronectin type III domain-containing protein 9 — Q8TBE3 (reviewed: Q8TBE3)

All UniProt accessions (2): Q8TBE3, E5RIJ1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001001343* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003961	FN3_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily

UniProt features (8 total): sequence variant 3, chain 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TBE3-F1	67.33	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 54 (showing top): AAAYRNCTG_UNKNOWN, TGCTGAY_UNKNOWN, PPAR_DR1_Q2, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, TGGAAA_NFAT_Q4_01, RYTGCNWTGGNR_UNKNOWN, HSF2_01, MIKKELSEN_MCV6_ICP_WITH_H3K27ME3, HSF1_01, PHESSE_TARGETS_OF_APC_AND_MBD2_UP, NFE2L2.V2, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_DN, SUPT16H_TARGET_GENES, MIR126_5P, MIR4306

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

242 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FNDC9	SMIM28	A0A1B0GU29	582
FNDC9	PROKR2	Q8NFJ6	535
FNDC9	ANKFN1	Q8N957	430
FNDC9	VWA3A	A6NCI4	419
FNDC9	FANK1	Q8TC84	406
FNDC9	ZNF446	Q9NWS9	380
FNDC9	RSKR	Q96LW2	376
FNDC9	UBTD1	Q9HAC8	372
FNDC9	ZNF814	B7Z6K7	371
FNDC9	SIRAL2	Q9NWS6	368
FNDC9	A0A0B4J1T7	A0A0B4J1T7	348
FNDC9	CFAP97	Q9P2B7	326
FNDC9	FNDC10	F2Z333	324
FNDC9	SERINC2	Q96SA4	308
FNDC9	MAP3K19	Q56UN5	307

IntAct

283 interactions, top by confidence:

A	B	Type	Score
FAM3C	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
ATP6V0C	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
CACNG1	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
CD302	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
MYADM	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
SLC30A8	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
UPK2	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
LPAR3	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
STX8	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
ITM2A	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
FNDC9	FAM3C	psi-mi:“MI:0915”(physical association)	0.560
FNDC9	TMEM60	psi-mi:“MI:0915”(physical association)	0.560
VAMP5	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
FNDC9	MYADM	psi-mi:“MI:0915”(physical association)	0.560
FNDC9	EXTL1	psi-mi:“MI:0915”(physical association)	0.560
ATXN1	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
AQP1	FNDC9	psi-mi:“MI:0915”(physical association)	0.560
CXCL16	FNDC9	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (89): FNDC9 (Synthetic Lethality), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid), FNDC9 (Two-hybrid)

ESM2 similar proteins: A0JNM1, A1L1A6, A6QNY1, A6QQC6, B0CLX4, B2RTN2, B8JI67, D3YX43, O02733, O88324, P01881, P01883, P12342, P21995, P26898, P86176, Q01151, Q0VCB1, Q0VFL4, Q2YDG7, Q3U0X8, Q5RCS3, Q5UKY4, Q6AXW8, Q6PCB8, Q7TMJ8, Q7TQM3, Q7TSN7, Q8BJN4, Q8IW00, Q8N7X8, Q8R526, Q8TBE3, Q8TDX9, Q8VCP9, Q8VD31, Q91V87, Q91ZV2, Q91ZV3, Q96FE7

Diamond homologs: Q8BJN4, Q8TBE3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	5
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

401 predictions. Top by Δscore:

Variant	Effect	Δscore
5:157343539:CGATT:C	acceptor_gain	0.9900
5:157343542:TT:T	acceptor_gain	0.9900
5:157343544:C:CC	acceptor_gain	0.9900
5:157343551:C:CT	acceptor_gain	0.9900
5:157343552:A:T	acceptor_gain	0.9900
5:157343543:TCT:T	acceptor_loss	0.9800
5:157343545:T:G	acceptor_loss	0.9800
5:157343551:C:T	acceptor_gain	0.9800
5:157345535:TCTTA:T	donor_loss	0.9800
5:157345536:CTTA:C	donor_loss	0.9800
5:157345537:TTA:T	donor_loss	0.9800
5:157345538:TA:T	donor_loss	0.9800
5:157345539:A:AG	donor_loss	0.9800
5:157345540:C:CT	donor_loss	0.9800
5:157343557:C:CT	acceptor_gain	0.9400
5:157345534:GTCTT:G	donor_loss	0.9400
5:157342621:A:AG	acceptor_gain	0.9300
5:157342624:T:A	acceptor_gain	0.9300
5:157343558:A:T	acceptor_gain	0.9200
5:157345539:A:AC	donor_gain	0.9200
5:157345540:C:CC	donor_gain	0.9200
5:157342605:A:AG	acceptor_gain	0.9000
5:157342622:A:G	acceptor_gain	0.9000
5:157343546:G:C	acceptor_loss	0.8900
5:157342596:T:G	acceptor_gain	0.8800
5:157342621:AACT:A	acceptor_gain	0.8600
5:157342606:A:G	acceptor_gain	0.8500
5:157343587:G:GG	donor_gain	0.8500
5:157344837:G:A	donor_gain	0.8500
5:157342594:A:AG	acceptor_gain	0.8400

AlphaMissense

1470 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:157343262:A:C	F92C	0.997
5:157343170:A:G	C123R	0.996
5:157343486:C:A	W17C	0.995
5:157343486:C:G	W17C	0.995
5:157343261:G:C	F92L	0.994
5:157343261:G:T	F92L	0.994
5:157343262:A:G	F92S	0.994
5:157343263:A:G	F92L	0.994
5:157343488:A:G	W17R	0.994
5:157343488:A:T	W17R	0.994
5:157343143:A:G	C132R	0.993
5:157343429:C:A	W36C	0.991
5:157343429:C:G	W36C	0.991
5:157343314:A:G	C75R	0.990
5:157343270:G:C	C89W	0.989
5:157343323:A:C	Y72D	0.989
5:157343271:C:T	C89Y	0.988
5:157343312:G:C	C75W	0.988
5:157343499:G:T	A13D	0.987
5:157343313:C:T	C75Y	0.986
5:157343313:C:G	C75S	0.985
5:157343314:A:T	C75S	0.985
5:157343470:A:G	C23R	0.985
5:157343271:C:G	C89S	0.984
5:157343272:A:T	C89S	0.984
5:157343272:A:G	C89R	0.983
5:157343147:G:C	F130L	0.982
5:157343147:G:T	F130L	0.982
5:157343149:A:G	F130L	0.982
5:157343304:C:T	C78Y	0.982

dbSNP variants (sampled 300 via entrez): RS1000195812 (5:157346758 A>G,T), RS1000996445 (5:157342405 T>G), RS1001134978 (5:157342162 G>A), RS1002137431 (5:157343321 G>A,T), RS1002250015 (5:157341696 G>A), RS1002427986 (5:157347135 A>T), RS1003232305 (5:157344456 A>G), RS10037386 (5:157342641 C>T), RS10037485 (5:157343125 C>A,T), RS1004079254 (5:157343293 C>T), RS1004940514 (5:157342618 C>G), RS1005051156 (5:157344410 G>A), RS1005492345 (5:157344691 G>A,T), RS1005606070 (5:157345285 T>C), RS1005658240 (5:157344980 A>G)

Disease associations

OMIM: gene `` | 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
GCST009798_48	Asthma	2.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
terbufos	increases methylation	1
Fonofos	increases methylation	1
Folic Acid	decreases expression	1
Parathion	increases methylation	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Asbestos, Serpentine	decreases expression	1

Clinical trials (associated diseases)

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