FKBP7

Summary

FKBP7 (FKBP prolyl isomerase 7, HGNC:3723) is a protein-coding gene on chromosome 2q31.2, encoding Peptidyl-prolyl cis-trans isomerase FKBP7 (Q9Y680). PPIases accelerate the folding of proteins during protein synthesis.

The protein encoded by this gene belongs to the FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) family. Members of this family exhibit PPIase activity and function as molecular chaperones. A similar protein in mouse is located in the endoplasmic reticulum and binds calcium.

Source: NCBI Gene 51661 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 42 total
• MANE Select transcript: NM_181342

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3723
Approved symbol	FKBP7
Name	FKBP prolyl isomerase 7
Location	2q31.2
Locus type	gene with protein product
Status	Approved
Aliases	FKBP23
Ensembl gene	ENSG00000079150
Ensembl biotype	protein_coding
OMIM	607062
Entrez	51661

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 nonsense_mediated_decay, 4 protein_coding, 1 retained_intron

ENST00000233092, ENST00000412612, ENST00000419184, ENST00000424785, ENST00000434643, ENST00000435079, ENST00000464248, ENST00000470945, ENST00000685403, ENST00000691082, ENST00000691586, ENST00000692292

RefSeq mRNA: 3 — MANE Select: NM_181342 NM_001135212, NM_001410972, NM_181342

CCDS: CCDS2280, CCDS46462, CCDS92911

Canonical transcript exons

ENST00000424785 — 4 exons

Exon	Start	End
ENSE00001754743	178463664	178465931
ENSE00001858280	178478279	178478600
ENSE00003582405	178477062	178477213
ENSE00003626681	178469652	178469785

Expression profiles

Bgee: expression breadth ubiquitous, 230 present calls, max score 96.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.1978 / max 272.3554, expressed in 1600 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
32016	20.9534	1597
32015	0.2443	97

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	96.94	gold quality
calcaneal tendon	UBERON:0003701	96.42	gold quality
left ovary	UBERON:0002119	93.96	gold quality
right ovary	UBERON:0002118	93.66	gold quality
sperm	CL:0000019	93.51	gold quality
ovary	UBERON:0000992	92.44	gold quality
tendon	UBERON:0000043	92.11	gold quality
tendon of biceps brachii	UBERON:0008188	91.97	gold quality
smooth muscle tissue	UBERON:0001135	91.94	gold quality
endocervix	UBERON:0000458	91.13	gold quality
tibia	UBERON:0000979	90.84	gold quality
descending thoracic aorta	UBERON:0002345	90.84	gold quality
thoracic aorta	UBERON:0001515	90.13	gold quality
ascending aorta	UBERON:0001496	90.09	gold quality
body of uterus	UBERON:0009853	89.87	gold quality
right coronary artery	UBERON:0001625	89.09	gold quality
endometrium	UBERON:0001295	89.07	gold quality
left uterine tube	UBERON:0001303	88.85	gold quality
aorta	UBERON:0000947	88.84	gold quality
uterus	UBERON:0000995	88.22	gold quality
popliteal artery	UBERON:0002250	88.03	gold quality
tibial artery	UBERON:0007610	88.01	gold quality
left coronary artery	UBERON:0001626	87.93	gold quality
gall bladder	UBERON:0002110	87.52	gold quality
coronary artery	UBERON:0001621	87.06	gold quality
left testis	UBERON:0004533	86.79	gold quality
right testis	UBERON:0004534	86.61	gold quality
female reproductive system	UBERON:0000474	86.52	gold quality
testis	UBERON:0000473	86.26	gold quality
myometrium	UBERON:0001296	86.24	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	17.25
E-ANND-3	yes	15.02
E-MTAB-9388	yes	8.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting FKBP7, 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-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-6499-3P	99.90	66.38	1212
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4496	99.88	68.89	2236

Literature-anchored findings (GeneRIF, showing 3)

• RUNX1 and FKBP7, involved in erythropoesis and muscle protein synthesis, respectively, are related to change in cardiorespiratory fitness in response to exercise. (PMID:23899896)
• observed changes in activity of six rER-resident PPIases, cyclophilin B (encoded by the PPIB gene), FKBP13 (FKBP2), FKBP19 (FKBP11), FKBP22 (FKBP14), FKBP23 (FKBP7), and FKBP65 (FKBP10), due to posttranslational modifications of proline residues in the substrate. (PMID:28385890)
• Hippocampal volume, FKBP5 genetic risk alleles, and childhood trauma interact to increase vulnerability to chronic multisite musculoskeletal pain. (PMID:35444168)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	fkbp7	ENSDARG00000010962
mus_musculus	Fkbp7	ENSMUSG00000002732
rattus_norvegicus	Fkbp7	ENSRNOG00000011758
drosophila_melanogaster	Fkbp39	FBGN0013269
caenorhabditis_elegans		WBGENE00001429
caenorhabditis_elegans	fkb-5	WBGENE00001430

Paralogs (18): FKBP4 (ENSG00000004478), FKBP6 (ENSG00000077800), FKBP1A (ENSG00000088832), FKBP5 (ENSG00000096060), FKBP3 (ENSG00000100442), FKBP8 (ENSG00000105701), FKBP14 (ENSG00000106080), FKBP15 (ENSG00000119321), FKBP1B (ENSG00000119782), FKBP9 (ENSG00000122642), TTC9 (ENSG00000133985), FKBP11 (ENSG00000134285), FKBP10 (ENSG00000141756), TTC9C (ENSG00000162222), FKBP2 (ENSG00000173486), TTC9B (ENSG00000174521), FKBP1C (ENSG00000198225), FKBPL (ENSG00000204315)

Protein

Protein identifiers

Peptidyl-prolyl cis-trans isomerase FKBP7 — Q9Y680 (reviewed: Q9Y680)

Alternative names: 23 kDa FK506-binding protein, FK506-binding protein 7, Rotamase

All UniProt accessions (6): Q9Y680, A0A8I5KRR8, B4DRE2, F8WBF2, F8WCU2, H7BZJ4

UniProt curated annotations — full annotation on UniProt →

Function. PPIases accelerate the folding of proteins during protein synthesis.

Subcellular location. Endoplasmic reticulum lumen.

Post-translational modifications. Glycosylated.

Miscellaneous. Binds calcium. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y680-2	2	yes
Q9Y680-3	3
Q9Y680-1	1

RefSeq proteins (3): NP_001128684, NP_001397901, NP_851939* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001179	PPIase_FKBP_dom	Domain
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR046357	PPIase_dom_sf	Homologous_superfamily
IPR052273	PPIase_FKBP	Family

Pfam: PF00254, PF13202

Catalyzed reactions (Rhea), 1 shown:

• [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0) (RHEA:16237)

UniProt features (22 total): binding site 9, splice variant 3, domain 3, sequence conflict 2, signal peptide 1, chain 1, glycosylation site 1, region of interest 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y680-F1	86.12	0.68

Functional residue map

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

Ligand- & substrate-binding residues (9): 164; 169; 202; 204; 206; 213; 158; 160; 162

Glycosylation sites (1): 45

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, WANG_LMO4_TARGETS_DN, ROZANOV_MMP14_TARGETS_UP, E4F1_Q6, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FISCHER_DREAM_TARGETS, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, GOCC_ENDOPLASMIC_RETICULUM_LUMEN, PAX2_02, WANG_SMARCE1_TARGETS_UP, GOMF_CIS_TRANS_ISOMERASE_ACTIVITY, GOMF_MACROLIDE_BINDING, GOMF_AMIDE_BINDING, GOMF_ISOMERASE_ACTIVITY

GO Biological Process (0):

GO Molecular Function (6): peptidyl-prolyl cis-trans isomerase activity (GO:0003755), calcium ion binding (GO:0005509), FK506 binding (GO:0005528), protein binding (GO:0005515), isomerase activity (GO:0016853), metal ion binding (GO:0046872)

GO Cellular Component (2): endoplasmic reticulum (GO:0005783), endoplasmic reticulum lumen (GO:0005788)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cis-trans isomerase activity	1
catalytic activity, acting on a protein	1
metal ion binding	1
macrolide binding	1
binding	1
catalytic activity	1
cation binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
endoplasmic reticulum	1
intracellular organelle lumen	1

Protein interactions and networks

STRING

1636 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FKBP7	HSPA5	P11021	551
FKBP7	FKBP15	Q5T1M5	513
FKBP7	HSPA4	P34932	476
FKBP7	LARP1	Q6PKG0	470
FKBP7	SUMF2	Q8NBJ7	439
FKBP7	PLEKHA3	Q9HB20	394
FKBP7	OS9	Q13438	391
FKBP7	NATD1	Q8N6N6	387
FKBP7	ERP44	Q9BS26	370
FKBP7	FAM76A	Q8TAV0	352
FKBP7	DERL2	Q9GZP9	350
FKBP7	PPIB	P23284	350
FKBP7	PPIL3	Q9H2H8	345
FKBP7	VPS39	Q96JC1	338
FKBP7	ENPP4	Q9Y6X5	334

IntAct

259 interactions, top by confidence:

A	B	Type	Score
FKBP7	SGTA	psi-mi:“MI:0915”(physical association)	0.720
SGTA	FKBP7	psi-mi:“MI:0915”(physical association)	0.720
PEX19	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
FKBP7	PEX19	psi-mi:“MI:0915”(physical association)	0.560
FAM3C	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
FKBP7	NPFFR2	psi-mi:“MI:0915”(physical association)	0.560
H4C7	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
TSPAN2	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
SNX1	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
TMEM108	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
CXCL16	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
YIPF6	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
THSD7B	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
RPRM	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
SNX12	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
GET3	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
TMEM86A	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
FARS2	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
DIABLO	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
JOSD2	FKBP7	psi-mi:“MI:0915”(physical association)	0.560
APOD	FKBP7	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (163): FKBP7 (Two-hybrid), FKBP7 (Two-hybrid), FKBP7 (Affinity Capture-MS), FKBP7 (Affinity Capture-MS), ATP5J (Co-fractionation), CARHSP1 (Co-fractionation), DUT (Co-fractionation), FKBP7 (Co-fractionation), FKBP7 (Co-fractionation), FKBP7 (Co-fractionation), FKBP7 (Co-fractionation), FKBP7 (Co-fractionation), GSTO1 (Co-fractionation), HINT1 (Co-fractionation), PPA1 (Co-fractionation)

ESM2 similar proteins: H0ZAB5, O35548, O46638, O54998, O61394, O73798, O77636, P0C1J4, P0C1J5, P0CP96, P0CP97, P26884, P29120, P32472, P34714, P45878, P51512, P59024, P63239, P63240, P70419, P78536, Q00688, Q14435, Q19267, Q32PA9, Q38935, Q38936, Q41649, Q5BKL9, Q5R941, Q5RET2, Q5RF88, Q5ZKE5, Q62446, Q66JA6, Q6CGG3, Q6CUZ8, Q6FSC1, Q6WV20

Diamond homologs: A6QQ71, D3ZQF4, F6PHZ6, O42123, O42993, O46638, O54998, O75344, O94746, O95302, P0A0W2, P0A0W3, P0C1J3, P0C1J4, P0C1J5, P0C1J6, P0CP94, P0CP95, P0CP96, P0CP97, P18203, P20080, P20081, P26883, P26884, P26885, P27124, P28870, P30416, P30417, P32472, P44760, P45523, P45878, P48375, P54397, P56989, P57599, P62942, P62943

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

748 predictions. Top by Δscore:

Variant	Effect	Δscore
2:178465928:TTAT:T	acceptor_gain	1.0000
2:178465931:TC:T	acceptor_loss	1.0000
2:178465932:C:CC	acceptor_gain	1.0000
2:178465932:C:CG	acceptor_loss	1.0000
2:178465933:T:G	acceptor_loss	1.0000
2:178469647:ATTAC:A	donor_loss	1.0000
2:178469648:TTAC:T	donor_loss	1.0000
2:178469649:TACCT:T	donor_loss	1.0000
2:178469650:ACCTC:A	donor_loss	1.0000
2:178469786:C:CC	acceptor_gain	1.0000
2:178477210:CCGG:C	acceptor_gain	1.0000
2:178477211:CGG:C	acceptor_gain	1.0000
2:178477211:CGGC:C	acceptor_gain	1.0000
2:178477214:C:CC	acceptor_gain	1.0000
2:178478275:CTACC:C	donor_loss	1.0000
2:178478276:TAC:T	donor_loss	1.0000
2:178478277:ACCTG:A	donor_loss	1.0000
2:178478278:C:CA	donor_loss	1.0000
2:178465927:TTTAT:T	acceptor_gain	0.9900
2:178465929:TAT:T	acceptor_gain	0.9900
2:178467778:A:AC	donor_gain	0.9900
2:178467779:C:CC	donor_gain	0.9900
2:178469651:CCT:C	donor_gain	0.9900
2:178469783:CTG:C	acceptor_gain	0.9900
2:178477055:ATCTT:A	donor_loss	0.9900
2:178477056:TCTTA:T	donor_loss	0.9900
2:178477057:CTTA:C	donor_loss	0.9900
2:178477058:TTA:T	donor_loss	0.9900
2:178477059:TACCA:T	donor_loss	0.9900
2:178477060:A:AC	donor_gain	0.9900

AlphaMissense

1486 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:178477109:C:G	R109P	1.000
2:178477082:G:T	A118E	0.997
2:178477097:A:T	I113K	0.997
2:178477213:G:C	S74R	0.997
2:178477213:G:T	S74R	0.997
2:178478280:T:G	S74R	0.997
2:178469737:A:G	L141P	0.996
2:178469755:A:C	L135W	0.996
2:178469762:C:G	A133P	0.996
2:178477148:A:G	L96P	0.996
2:178477152:C:G	G95R	0.996
2:178478315:C:T	G62D	0.996
2:178469748:A:C	F137L	0.995
2:178469748:A:T	F137L	0.995
2:178469750:A:G	F137L	0.995
2:178477097:A:C	I113R	0.995
2:178477124:C:G	C104S	0.995
2:178477125:A:T	C104S	0.995
2:178477139:G:T	A99D	0.995
2:178478333:A:G	L56P	0.995
2:178469755:A:G	L135S	0.994
2:178477183:C:A	W84C	0.994
2:178477183:C:G	W84C	0.994
2:178478327:G:T	A58D	0.994
2:178478328:C:G	A58P	0.994
2:178478350:G:C	S50R	0.994
2:178478350:G:T	S50R	0.994
2:178478352:T:G	S50R	0.994
2:178469665:A:G	L165P	0.993
2:178469737:A:T	L141H	0.993

dbSNP variants (sampled 300 via entrez): RS1000025434 (2:178468864 A>G), RS1000271469 (2:178473177 TAAC>T), RS1000955904 (2:178477626 T>A), RS1001072054 (2:178477876 A>G), RS1001167856 (2:178478674 C>A,T), RS1001251501 (2:178471227 T>TA), RS1001260022 (2:178475526 G>A), RS1001283949 (2:178478945 G>A), RS1001325662 (2:178470071 G>A,C), RS1001477567 (2:178464689 T>A), RS1001689822 (2:178472361 C>T), RS1001721802 (2:178472099 A>G), RS1002119309 (2:178472662 A>C,G), RS1002272026 (2:178476480 T>C), RS1002289949 (2:178477527 C>T)

Disease associations

OMIM: gene MIM:607062 | disease phenotypes: MIM:604145, MIM:608807

GenCC curated gene-disease

Mondo (2): dilated cardiomyopathy 1G (MONDO:0011400), autosomal recessive limb-girdle muscular dystrophy type 2J (MONDO:0012127)

Orphanet (2): Titin-related limb-girdle muscular dystrophy R10 (Orphanet:140922), Familial isolated dilated cardiomyopathy (Orphanet:154)

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003332_1	Rapid functional decline in sporadic amyotrophic lateral sclerosis	2.000000e-08
GCST006414_71	Atrial fibrillation	7.000000e-25
GCST006585_2065	Blood protein levels	2.000000e-39
GCST010002_405	Refractive error	1.000000e-70
GCST90000025_831	Appendicular lean mass	3.000000e-10
GCST90011898_91	Alanine aminotransferase levels	1.000000e-08
GCST90011899_82	Aspartate aminotransferase levels	6.000000e-16

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007784	functional decline measurement
EFO:0004980	appendicular lean mass
EFO:0004736	aspartate aminotransferase measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C565824	Cardiomyopathy, Dilated, 1g (supp.)
C563854	Muscular Dystrophy, Limb-Girdle, Type 2J (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
sodium arsenite	increases expression, decreases expression, affects cotreatment	4
bisphenol F	increases expression, affects cotreatment	2
Cyclosporine	decreases expression	2
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	affects cotreatment, increases expression	1
trichostatin A	increases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	decreases expression	1
cupric oxide	decreases expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
K 7174	decreases expression	1
bisphenol B	increases expression	1
abrine	decreases expression	1
bisphenol S	increases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
bisphenol AF	increases expression	1
Sunitinib	decreases expression	1
Vorinostat	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Drugs, Chinese Herbal	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05989620	Not specified	RECRUITING	Long-Term Development of Muscular Dystrophy Outcome Assessments