FNBP1

Summary

FNBP1 (formin binding protein 1, HGNC:17069) is a protein-coding gene on chromosome 9q34.11, encoding Formin-binding protein 1 (Q96RU3). May act as a link between RND2 signaling and regulation of the actin cytoskeleton.

The protein encoded by this gene is a member of the formin-binding-protein family. The protein contains an N-terminal Fer/Cdc42-interacting protein 4 (CIP4) homology (FCH) domain followed by a coiled-coil domain, a proline-rich motif, a second coiled-coil domain, a Rho family protein-binding domain (RBD), and a C-terminal SH3 domain. This protein binds sorting nexin 2 (SNX2), tankyrase (TNKS), and dynamin; an interaction between this protein and formin has not been demonstrated yet in human.

Source: NCBI Gene 23048 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 100 total
• MANE Select transcript: NM_015033

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17069
Approved symbol	FNBP1
Name	formin binding protein 1
Location	9q34.11
Locus type	gene with protein product
Status	Approved
Aliases	FBP17, KIAA0554
Ensembl gene	ENSG00000187239
Ensembl biotype	protein_coding
OMIM	606191
Entrez	23048

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 20 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000355681, ENST00000446176, ENST00000449089, ENST00000462766, ENST00000478129, ENST00000482107, ENST00000491905, ENST00000699492, ENST00000703532, ENST00000703533, ENST00000703558, ENST00000703559, ENST00000703560, ENST00000907739, ENST00000907740, ENST00000907741, ENST00000907742, ENST00000907743, ENST00000918044, ENST00000918045, ENST00000946014, ENST00000946015, ENST00000946016, ENST00000946017

RefSeq mRNA: 3 — MANE Select: NM_015033 NM_001363755, NM_001411018, NM_015033

CCDS: CCDS48040, CCDS87699, CCDS94507

Canonical transcript exons

ENST00000446176 — 17 exons

Exon	Start	End
ENSE00000927326	129927195	129927341
ENSE00000927327	129929567	129929695
ENSE00000927329	129958491	129958553
ENSE00001177865	129957360	129957464
ENSE00001457749	129887187	129890546
ENSE00001457750	129895838	129895996
ENSE00001610071	129994843	129994958
ENSE00001639970	129915966	129915980
ENSE00001660193	129978465	129978612
ENSE00003474886	129900426	129900547
ENSE00003483788	129908890	129908999
ENSE00003488746	129902869	129903001
ENSE00003561808	129924960	129925157
ENSE00003589670	129979318	129979374
ENSE00003989342	130042952	130043189
ENSE00003989343	129899965	129900101
ENSE00003989344	129923844	129924026

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 98.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.1652 / max 1356.8538, expressed in 1788 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102794	19.9075	1712
102782	5.4023	1233
102795	5.1772	1567
102793	0.9769	464
205636	0.7036	377
102777	0.6947	118
102775	0.3012	49
102776	0.2752	63
102779	0.1888	76
102774	0.1869	45

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	98.47	gold quality
mucosa of stomach	UBERON:0001199	98.24	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.01	gold quality
lower esophagus	UBERON:0013473	97.98	gold quality
cerebellar hemisphere	UBERON:0002245	97.90	gold quality
cerebellum	UBERON:0002037	97.87	gold quality
cerebellar cortex	UBERON:0002129	97.84	gold quality
saphenous vein	UBERON:0007318	97.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	97.65	gold quality
paraflocculus	UBERON:0005351	97.63	gold quality
inferior vagus X ganglion	UBERON:0005363	97.63	gold quality
thymus	UBERON:0002370	97.57	gold quality
colonic epithelium	UBERON:0000397	97.51	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.36	gold quality
sural nerve	UBERON:0015488	97.27	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.23	gold quality
seminal vesicle	UBERON:0000998	97.18	gold quality
middle frontal gyrus	UBERON:0002702	97.11	gold quality
inferior olivary complex	UBERON:0002127	97.08	gold quality
bone marrow cell	CL:0002092	96.99	gold quality
lymph node	UBERON:0000029	96.69	gold quality
medulla oblongata	UBERON:0001896	96.66	gold quality
calcaneal tendon	UBERON:0003701	96.65	gold quality
secondary oocyte	CL:0000655	96.60	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	96.56	gold quality
lateral globus pallidus	UBERON:0002476	96.53	gold quality
mucosa of urinary bladder	UBERON:0001259	96.45	gold quality
leukocyte	CL:0000738	96.38	gold quality
mononuclear cell	CL:0000842	96.35	gold quality
monocyte	CL:0000576	96.34	gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 10.

Experiment	Marker?	Max mean expression
E-MTAB-8142	yes	78.24
E-GEOD-135922	yes	26.96
E-HCAD-13	yes	22.28
E-CURD-112	yes	19.67
E-HCAD-1	yes	19.33
E-MTAB-6701	yes	19.20
E-HCAD-10	yes	8.56
E-MTAB-6678	yes	7.54
E-CURD-119	yes	4.67
E-MTAB-5061	no	3.69
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 21)

• Rat rapostlin protein has 93% aa identity to human FBP17. (PMID:12244061)
• FNBP1 family proteins (FNBP1 and TRIP10) consist of FCH, FBH and SH3 domains. (PMID:12736724)
• co-immunoprecipitation of endogenous proteins in 293T cells confirms physiological relevance of TNKS as interaction partner of FBP17 (PMID:14596906)
• FBP17 interacts with dynamin and regulates endocytosis by forming vesicotubular structures (PMID:15252009)
• Data indicate that PCH protein family members such as FBP17 couple membrane deformation to actin cytoskeleton reorganization in various cellular processes. (PMID:16418535)
• FBP17 is recruited to clathrin-coated pits in the late stage of endocytosis, indicating its physiological role. (PMID:17512409)
• N-WASP-WIP complex-mediated actin polymerization is activated by phosphatidylserine-containing membranes depending on membrane curvature in the presence of Toca-1 or FBP17 and in the absence of Cdc42 and phosphatidylinositol (4,5)-bisphosphate. (PMID:18923421)
• formin-binding protein 17 (FBP17) recruits WASP, WASP-interacting protein (WIP), and dynamin-2 to the plasma membrane and that this recruitment is necessary for the formation of podosomes and phagocytic cups. (PMID:19155218)
• Results suggest a functional link between FBP17-dependent membrane tubulation and clathrin-dependent budding. Clathrin spatially directs membrane invaginations that lead to the generation of endocytic vesicles larger than those enclosed by the coat. (PMID:20729836)
• F-BAR protein Rapostlin, whose activity is regulated by Rnd2, plays a key role in spine formation through the regulation of membrane dynamics. (PMID:21768103)
• Knockdown of PSTPIP2 inmacrophages enhances the assembly of FBP17, leading to’hyperactivation’ of actin nucleation at podosomes and ECM degradation. (PMID:23525018)
• FBP17 is the local activator of actin polymerization that is inhibited by PM tension in the feedback loop that regulates cell migration. (PMID:25938814)
• Results suggest that FBP17 is highly expressed in breast cancer cells and facilitates the invasion of breast cancer cells. (PMID:29651632)
• FBP17 and CIP4 prime the membrane of resting cells for fast endophilin-mediated endocytosis by recruiting the 5’-lipid phosphatase SHIP2 and lamellipodin to mediate the local production of phosphatidylinositol-3,4-bisphosphate and endophilin pre-enrichment. (PMID:30061681)
• Study shows that plasma membrane (PM) mechanoadaptation is controlled by a tension-sensing pathway composed of c-Abl tyrosine kinase and membrane curvature regulator FBP17. FBP17 is recruited to caveolae to induce the formation of caveolar rosettes. FBP17 deficient cells have reduced rosette density, lack PM tension buffering capacity under osmotic shock, and cannot adapt to mechanical strain. (PMID:31862885)
• High formin binding protein 17 (FBP17) expression indicates poor differentiation and invasiveness of ductal carcinomas. (PMID:32665637)
• Sp1-Induced FNBP1 Drives Rigorous 3D Cell Motility in EMT-Type Gastric Cancer Cells. (PMID:34202606)
• Membrane tension sensing molecule-FNBP1 is a prognostic biomarker related to immune infiltration in BRCA, LUAD and STAD. (PMID:34998385)
• Wild-type p53 suppresses formin-binding protein-17 (FBP17) to reduce invasion. (PMID:35134126)
• FNBP1 Facilitates Cervical Cancer Cell Survival by the Constitutive Activation of FAK/PI3K/AKT/mTOR Signaling. (PMID:37566043)
• Formin Binding Protein 1 (FNBP1) regulates non-canonical Wnt signaling and vertebrate gastrulation. (PMID:38945423)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	fnbp1a	ENSDARG00000036156
danio_rerio	fnbp1b	ENSDARG00000096367
danio_rerio	fnbp1b	ENSDARG00000101028
mus_musculus	Fnbp1	ENSMUSG00000075415
rattus_norvegicus	Fnbp1	ENSRNOG00000008258
drosophila_melanogaster	Cip4	FBGN0035533
caenorhabditis_elegans		WBGENE00010663
caenorhabditis_elegans		WBGENE00017298

Paralogs (2): TRIP10 (ENSG00000125733), FNBP1L (ENSG00000137942)

Protein

Protein identifiers

Formin-binding protein 1 — Q96RU3 (reviewed: Q96RU3)

Alternative names: Formin-binding protein 17

All UniProt accessions (8): A0A8V8TQ35, A0A994J3U5, A0A994J3V8, A0A994J4A3, A0A994J6U4, B7ZL13, H0Y7W6, Q96RU3

UniProt curated annotations — full annotation on UniProt →

Function. May act as a link between RND2 signaling and regulation of the actin cytoskeleton. Required to coordinate membrane tubulation with reorganization of the actin cytoskeleton during the late stage of clathrin-mediated endocytosis. Binds to lipids such as phosphatidylinositol 4,5-bisphosphate and phosphatidylserine and promotes membrane invagination and the formation of tubules. Also enhances actin polymerization via the recruitment of WASL/N-WASP, which in turn activates the Arp2/3 complex. Actin polymerization may promote the fission of membrane tubules to form endocytic vesicles. May be required for the lysosomal retention of FASLG/FASL.

Subunit / interactions. Interacts specifically with GTP-bound RND2 and CDC42. Interacts with PDE6G and microtubules. Homodimerizes, the dimers can polymerize end-to-end to form filamentous structures. Interacts with AKAP9, ARHGAP17, DAAM1, DIAPH1, DIAPH2, DNM1, DNM2, DNM3, FASLG/FASL, SNX2 and WASL/N-WASP. May interact with TNKS.

Subcellular location. Cytoplasm. Cytoskeleton. Cell cortex. Lysosome. Cytoplasmic vesicle. Cell membrane. Membrane. Clathrin-coated pit.

Tissue specificity. Very highly expressed in the epithelial cells of the gastrointestinal tract, respiratory, reproductive and urinary systems. Also highly expressed in brown adipose tissue, cardiomyocytes, enteric ganglia and glucagon producing cells of the pancreas. Expressed in germ cells of the testis and all regions of the brain.

Disease relevance. A chromosomal aberration involving FNBP1 is found in acute leukemias. Translocation t(9;11)(q34;q23) with KMT2A/MLL1. The relatively low incidence of the KMT2A/MLL1-FNBP1 fusion protein in acute leukemia may reflect the marginal capacity of this fusion protein to induce cellular transformation.

Domain organisation. The F-BAR domain binds the phospholipid membrane with its concave surface. The end-to-end polymerization of dimers of these domains provides a curved surface that fits best membranes with around 600 A diameter, and may drive tubulation.

Similarity. Belongs to the FNBP1 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q96RU3-1	1	yes
Q96RU3-2	2
Q96RU3-3	3
Q96RU3-4	4
Q96RU3-5	5

RefSeq proteins (3): NP_001350684, NP_001397947, NP_055848* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001060	FCH_dom	Domain
IPR001452	SH3_domain	Domain
IPR011072	HR1_rho-bd	Domain
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR031160	F_BAR_dom	Domain
IPR036028	SH3-like_dom_sf	Homologous_superfamily
IPR037449	FNBP1_F-BAR	Domain
IPR057870	HR1_TOCA	Domain

Pfam: PF00018, PF00611, PF25610

UniProt features (59 total): mutagenesis site 14, region of interest 13, modified residue 9, helix 7, splice variant 4, domain 3, coiled-coil region 2, compositionally biased region 2, chain 1, site 1, sequence variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2EFL	X-RAY DIFFRACTION	2.61

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96RU3-F1	79.06	0.62

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): 166 (mediates end-to-end attachment of dimers)

Post-translational modifications (9): 66, 110, 296, 299, 349, 359, 497, 500, 521

Mutagenesis-validated functional residues (14):

Position	Phenotype
7	impairs membrane tubulation but does not affect lipid-binding.
33	abolishes membrane invagination.
33	impairs lipid-binding and induction of membrane tubulation; when associated with q-35.
35	impairs lipid-binding and induction of membrane tubulation; when associated with q-33.
51–52	impairs lipid-binding and induction of membrane tubulation.
113–114	impairs lipid-binding and induction of membrane tubulation.
165	abolishes membrane invagination.
166	abolishes membrane invagination.
168	no significant effect.
210	disrupts helix kink and moderately increases diameter of the induced tubular membrane.
515–520	abrogates interaction with tnks.
515	impairs interaction with tnks.
519	impairs interaction with tnks; when associated with a-515.
602	abrogates interaction with dnm1, dnm2 and dnm3.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-8856828	Clathrin-mediated endocytosis
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-9013406	RHOQ GTPase cycle
R-HSA-9013409	RHOJ GTPase cycle
R-HSA-9696270	RND2 GTPase cycle

MSigDB gene sets: 241 (showing top): GCACCTT_MIR18A_MIR18B, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GTGCCTT_MIR506, ONKEN_UVEAL_MELANOMA_UP, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, MODULE_285, BLALOCK_ALZHEIMERS_DISEASE_UP, GROSS_HYPOXIA_VIA_ELK3_UP, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, CREBP1_01

GO Biological Process (2): endocytosis (GO:0006897), signal transduction (GO:0007165)

GO Molecular Function (3): lipid binding (GO:0008289), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (9): lysosome (GO:0005764), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), clathrin-coated pit (GO:0005905), cell cortex (GO:0005938), cytoplasmic vesicle (GO:0031410), cytoplasm (GO:0005737), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RHO GTPase cycle	4
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
cellular anatomical structure	3
binding	2
membrane	2
cell periphery	2
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
protein binding	1
lytic vacuole	1
intracellular membraneless organelle	1
endomembrane system	1
intracellular vesicle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1244 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FNBP1	CDC42	P21181	844
FNBP1	WAS	P42768	822
FNBP1	SNX2	P82862	781
FNBP1	WASL	O00401	780
FNBP1	INPPL1	O15357	758
FNBP1	PACSIN2	Q9UNF0	757
FNBP1	CNOT12	Q9C0C2	741
FNBP1	FCHO2	Q0JRZ9	697
FNBP1	AMPH	P49418	678
FNBP1	WIPF1	O43516	670
FNBP1	FCHSD1	Q86WN1	670
FNBP1	RAPH1	Q70E73	666
FNBP1	ABI1	Q8IZP0	656
FNBP1	LASP1	Q14847	653
FNBP1	BIN1	O00499	652

IntAct

55 interactions, top by confidence:

A	B	Type	Score
FNBP1	FNBP1	psi-mi:“MI:0915”(physical association)	0.680
FNBP1	FNBP1	psi-mi:“MI:0407”(direct interaction)	0.680
SNX2	FNBP1	psi-mi:“MI:0915”(physical association)	0.660
FNBP1	SNX2	psi-mi:“MI:0403”(colocalization)	0.660
FNBP1	SNX2	psi-mi:“MI:0915”(physical association)	0.660
TNKS	FNBP1	psi-mi:“MI:0915”(physical association)	0.600
FNBP1	TNKS	psi-mi:“MI:0915”(physical association)	0.600
FNBP1	TNKS	psi-mi:“MI:0403”(colocalization)	0.600
GABARAP	IPO5	psi-mi:“MI:0914”(association)	0.590
FASLG	FNBP1	psi-mi:“MI:0915”(physical association)	0.590
FNBP1	FASLG	psi-mi:“MI:0915”(physical association)	0.590
FNBP1	DNM1	psi-mi:“MI:0915”(physical association)	0.580
DNM1	FNBP1	psi-mi:“MI:0915”(physical association)	0.580
DNM1	FNBP1	psi-mi:“MI:0403”(colocalization)	0.580
FNBP1	DNM2	psi-mi:“MI:0403”(colocalization)	0.500
FNBP1	DNM3	psi-mi:“MI:0403”(colocalization)	0.500
FNBP1	DNM2	psi-mi:“MI:0915”(physical association)	0.500
DNM3	FNBP1	psi-mi:“MI:0915”(physical association)	0.500
FNBP1	Inpp5d	psi-mi:“MI:0915”(physical association)	0.500
FNBP1	GABARAP	psi-mi:“MI:0915”(physical association)	0.500
FNBP1	FNBP1L	psi-mi:“MI:0914”(association)	0.500
FNBP1L	FNBP1	psi-mi:“MI:0915”(physical association)	0.500
ADAM8	FNBP1	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (143): FNBP1 (Affinity Capture-RNA), FNBP1 (Affinity Capture-RNA), FCHO1 (Co-fractionation), FNBP1 (Co-fractionation), MYO1E (Co-fractionation), SF3A1 (Co-fractionation), DNM1 (Co-localization), DNM2 (Co-localization), FNBP1 (Proximity Label-MS), FNBP1 (Affinity Capture-MS), FNBP1 (Affinity Capture-RNA), FNBP1 (Affinity Capture-RNA), FNBP1 (Affinity Capture-MS), FNBP1 (Affinity Capture-Western), FNBP1 (Affinity Capture-Western)

ESM2 similar proteins: A1A4L0, A6H6A9, B4F779, G5E8V9, O35382, O60890, O95219, P0CAX5, P53365, P53367, Q08DP6, Q28E02, Q3ZCL5, Q4V7P7, Q566W7, Q5EAD0, Q5R4C2, Q5RCW6, Q5T0N5, Q5VWJ9, Q5ZJ17, Q60437, Q62824, Q6AY65, Q6GMN2, Q6PCS4, Q6Y5D8, Q6ZQ82, Q7YQL5, Q7YQL6, Q80TY0, Q8BHY8, Q8BKX1, Q8CE50, Q8K221, Q8K3G9, Q8K3H0, Q8N6S4, Q8NEU8, Q8R511

Diamond homologs: P97531, Q09746, Q15642, Q2HWF0, Q4P3H6, Q5RCJ1, Q5T0N5, Q5U3Q6, Q6DCZ7, Q6GNV5, Q6GUF4, Q80TY0, Q8CJ53, Q8K012, Q8R511, Q96RU3, X2JAU8, A7MBI0, O13154, O94291, P97369, Q15080, Q28E02, Q28GP7, Q2U4K2, Q3MPQ4, Q4R5U9, Q4V7P7, Q4V920, Q4VAA7, Q4WWS3, Q566W7, Q5R411, Q5VWJ9, Q61644, Q6C2S9, Q6CHY6, Q6NRL2, Q8CE50, Q8I4E2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 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
Clathrin-mediated endocytosis	8	25.2×	1e-07

GO biological processes:

GO term	Partners	Fold	FDR
endocytosis	6	19.0×	8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	67
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3196 predictions. Top by Δscore:

Variant	Effect	Δscore
9:129895833:AGCAC:A	donor_gain	1.0000
9:129895864:T:TA	donor_gain	1.0000
9:129895864:TCG:T	donor_gain	1.0000
9:129895886:AAC:A	donor_gain	1.0000
9:129899993:C:A	donor_gain	1.0000
9:129900108:A:T	acceptor_gain	1.0000
9:129900422:GTACC:G	donor_loss	1.0000
9:129900423:TA:T	donor_loss	1.0000
9:129900424:A:AC	donor_gain	1.0000
9:129900425:C:CC	donor_gain	1.0000
9:129900425:CCT:C	donor_gain	1.0000
9:129900431:ACGGT:A	donor_gain	1.0000
9:129900432:CGGTC:C	donor_gain	1.0000
9:129902864:CATA:C	donor_loss	1.0000
9:129902865:ATAC:A	donor_loss	1.0000
9:129902868:C:G	donor_loss	1.0000
9:129902997:CATCT:C	acceptor_gain	1.0000
9:129902998:ATCT:A	acceptor_gain	1.0000
9:129903000:CT:C	acceptor_gain	1.0000
9:129903000:CTCTG:C	acceptor_loss	1.0000
9:129903002:C:CC	acceptor_gain	1.0000
9:129903002:C:T	acceptor_loss	1.0000
9:129903003:T:A	acceptor_loss	1.0000
9:129908884:CTATA:C	donor_loss	1.0000
9:129908885:TATA:T	donor_loss	1.0000
9:129908886:ATAC:A	donor_loss	1.0000
9:129908887:TA:T	donor_loss	1.0000
9:129908888:AC:A	donor_loss	1.0000
9:129908889:CCTTT:C	donor_loss	1.0000
9:129908998:CC:C	acceptor_gain	1.0000

AlphaMissense

4137 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:129895882:A:T	V601D	1.000
9:129895922:A:G	W588R	1.000
9:129895922:A:T	W588R	1.000
9:129908944:A:G	L414P	1.000
9:129957431:C:G	A148P	1.000
9:129895920:C:A	W588C	0.999
9:129895920:C:G	W588C	0.999
9:129895948:A:T	V579D	0.999
9:129902984:A:G	M438T	0.999
9:129929628:A:G	L194P	0.999
9:129929683:C:G	A176P	0.999
9:129929691:C:G	R173P	0.999
9:129929695:C:G	A172P	0.999
9:129957367:A:T	V169D	0.999
9:129957382:A:T	V164D	0.999
9:129957422:C:G	A151P	0.999
9:129957445:C:G	R143P	0.999
9:129958498:A:G	L134P	0.999
9:129979369:A:G	L49P	0.999
9:129895867:A:T	V606D	0.998
9:129895909:C:G	R592P	0.998
9:129895921:C:G	W588S	0.998
9:129895924:C:T	G587D	0.998
9:129899969:A:C	F561L	0.998
9:129899969:A:T	F561L	0.998
9:129899971:A:G	F561L	0.998
9:129902973:A:C	Y442D	0.998
9:129908944:A:T	L414Q	0.998
9:129908971:A:G	L405P	0.998
9:129929662:C:G	A183P	0.998

dbSNP variants (sampled 300 via entrez): RS1000004886 (9:129897417 C>A,G,T), RS1000017958 (9:129957866 C>T), RS1000024941 (9:130052890 G>A), RS1000044463 (9:129887886 T>C), RS1000068609 (9:129970171 C>T), RS1000074816 (9:129898675 A>C), RS1000101559 (9:129893424 G>GA), RS1000107233 (9:130007758 G>A), RS1000116871 (9:129964033 G>A), RS1000124555 (9:130038183 T>G), RS1000132430 (9:130054622 C>A), RS1000154844 (9:129934803 C>T), RS1000155700 (9:130038553 C>A,T), RS1000158091 (9:129932578 A>G), RS1000166923 (9:130026509 A>T)

Disease associations

OMIM: gene MIM:606191 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST002989_7	LDL peak particle diameter (total fat intake interaction)	3.000000e-07
GCST003097_41	Pediatric autoimmune diseases	7.000000e-07
GCST004250_34	Alanine aminotransferase (ALT) levels after remission induction therapy in actute lymphoblastic leukemia (ALL)	4.000000e-06
GCST010279_2	Physiological dysregulation (Mahalanobis distance)	9.000000e-07
GCST012490_168	Femur bone mineral density x serum urate levels interaction	1.000000e-10
GCST90007004_5	Gut microbiota relative abundance (unassigned genus belonging to family Clostridiales)	2.000000e-06

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0007677	LDL peak particle diameter measurement
EFO:0007678	total fat intake measurement
EFO:0007965	response to combination chemotherapy
EFO:0003892	pulmonary function measurement
EFO:0004312	vital capacity
EFO:0004503	hematological measurement
EFO:0004732	lipoprotein measurement
EFO:0006941	grip strength measurement
EFO:0004531	urate measurement
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	affects expression, increases expression	4
Benzo(a)pyrene	decreases expression, decreases methylation	3
sodium arsenite	affects expression, increases expression	2
Cisplatin	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cadmium Chloride	increases expression	2
FR900359	increases phosphorylation	1
dicrotophos	increases expression	1
methylmercuric chloride	increases expression	1
bisphenol A	affects cotreatment, decreases expression	1
deoxynivalenol	decreases expression	1
methylselenic acid	increases expression	1
testosterone undecanoate	affects cotreatment, decreases expression	1
arsenite	decreases reaction, affects binding	1
cobaltous chloride	increases expression	1
nickel chloride	increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
aflatoxin B2	increases methylation	1
coumarin	decreases phosphorylation	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
sulphoraphene	decreases expression	1
dorsomorphin	increases expression, affects cotreatment	1
bisphenol S	affects cotreatment, decreases expression	1
(+)-JQ1 compound	increases expression	1
Zoledronic Acid	increases expression	1
Vorinostat	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Carbamazepine	affects expression	1

Clinical trials (associated diseases)

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