FARP1

Summary

FARP1 (FERM, ARH/RhoGEF and pleckstrin domain protein 1, HGNC:3591) is a protein-coding gene on chromosome 13q32.2, encoding FERM, ARHGEF and pleckstrin domain-containing protein 1 (Q9Y4F1). Functions as a guanine nucleotide exchange factor for RAC1.

This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10160 — RefSeq curated summary.

At a glance

• GWAS associations: 23
• Clinical variants (ClinVar): 271 total
• MANE Select transcript: NM_005766

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3591
Approved symbol	FARP1
Name	FERM, ARH/RhoGEF and pleckstrin domain protein 1
Location	13q32.2
Locus type	gene with protein product
Status	Approved
Aliases	CDEP, PLEKHC2, MGC87400, PPP1R75, GLCC1
Ensembl gene	ENSG00000152767
Ensembl biotype	protein_coding
OMIM	602654
Entrez	10160

Gene structure

Transcript identifiers

Ensembl transcripts: 63 — 30 protein_coding, 28 protein_coding_CDS_not_defined, 5 retained_intron

ENST00000319562, ENST00000376581, ENST00000423063, ENST00000427404, ENST00000457029, ENST00000457431, ENST00000490389, ENST00000593548, ENST00000593990, ENST00000594346, ENST00000594657, ENST00000595366, ENST00000595380, ENST00000595437, ENST00000595817, ENST00000596256, ENST00000596467, ENST00000596545, ENST00000596580, ENST00000596613, ENST00000597596, ENST00000597777, ENST00000598346, ENST00000598389, ENST00000598698, ENST00000599040, ENST00000599151, ENST00000600032, ENST00000600190, ENST00000600380, ENST00000600648, ENST00000601009, ENST00000601133, ENST00000601361, ENST00000601656, ENST00000601762, ENST00000601853, ENST00000602015, ENST00000602171, ENST00000602263, ENST00000602272, ENST00000627049, ENST00000871496, ENST00000871497, ENST00000871498, ENST00000871499, ENST00000871500, ENST00000871501, ENST00000871502, ENST00000871503, ENST00000871504, ENST00000871505, ENST00000871506, ENST00000922579, ENST00000922580, ENST00000922581, ENST00000922582, ENST00000922583, ENST00000922584, ENST00000922585, ENST00000922586, ENST00000964193, ENST00000964194

RefSeq mRNA: 3 — MANE Select: NM_005766 NM_001001715, NM_001286839, NM_005766

CCDS: CCDS32000, CCDS66572, CCDS9487

Canonical transcript exons

ENST00000319562 — 27 exons

Exon	Start	End
ENSE00001006991	98390812	98390880
ENSE00001006995	98439107	98439196
ENSE00001006999	98439961	98440043
ENSE00001007000	98395227	98395476
ENSE00001007008	98440670	98440836
ENSE00001007011	98435576	98435706
ENSE00001007013	98440123	98440235
ENSE00001007015	98438804	98438872
ENSE00001007017	98431043	98431280
ENSE00001279527	98446666	98446817
ENSE00001598019	98389957	98390120
ENSE00001621300	98446098	98446205
ENSE00001869358	98143094	98143492
ENSE00001871440	98448236	98455176
ENSE00002702764	98213220	98213413
ENSE00003493549	98411901	98412034
ENSE00003503227	98385667	98385814
ENSE00003571606	98409338	98409525
ENSE00003575735	98343762	98343866
ENSE00003589411	98410734	98410823
ENSE00003596683	98368117	98368195
ENSE00003598300	98393643	98393718
ENSE00003609972	98365395	98365437
ENSE00003659207	98388383	98388478
ENSE00003666123	98424572	98424650
ENSE00003691365	98377821	98377918
ENSE00003787131	98384730	98384844

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 98.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.0733 / max 725.4175, expressed in 1575 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135754	27.1434	1566
135755	5.6181	1432
135758	3.9851	1404
135759	1.7923	938
135753	0.9355	446
135756	0.8550	523
135760	0.7942	380
207082	0.5397	327
135757	0.4316	192
135752	0.3992	214

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
renal medulla	UBERON:0000362	98.67	gold quality
stromal cell of endometrium	CL:0002255	98.26	gold quality
adrenal tissue	UBERON:0018303	98.16	gold quality
corpus epididymis	UBERON:0004359	96.86	gold quality
cortical plate	UBERON:0005343	96.28	gold quality
adult mammalian kidney	UBERON:0000082	96.22	gold quality
ganglionic eminence	UBERON:0004023	96.17	gold quality
ventricular zone	UBERON:0003053	96.07	gold quality
metanephros cortex	UBERON:0010533	96.03	gold quality
colonic epithelium	UBERON:0000397	95.84	gold quality
kidney	UBERON:0002113	95.26	gold quality
embryo	UBERON:0000922	95.16	gold quality
right lobe of liver	UBERON:0001114	94.87	gold quality
parotid gland	UBERON:0001831	94.47	gold quality
thyroid gland	UBERON:0002046	94.14	gold quality
left lobe of thyroid gland	UBERON:0001120	94.11	gold quality
caput epididymis	UBERON:0004358	94.11	gold quality
right lobe of thyroid gland	UBERON:0001119	93.93	gold quality
tibia	UBERON:0000979	93.58	gold quality
metanephros	UBERON:0000081	93.38	gold quality
cortex of kidney	UBERON:0001225	93.25	gold quality
liver	UBERON:0002107	93.18	gold quality
body of pancreas	UBERON:0001150	93.15	gold quality
cauda epididymis	UBERON:0004360	93.09	gold quality
prostate gland	UBERON:0002367	93.02	gold quality
muscle layer of sigmoid colon	UBERON:0035805	92.80	gold quality
bronchial epithelial cell	CL:0002328	92.75	gold quality
pylorus	UBERON:0001166	92.66	gold quality
calcaneal tendon	UBERON:0003701	92.47	gold quality
stomach	UBERON:0000945	92.40	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-GEOD-180759	yes	7112.33
E-MTAB-11121	yes	589.14
E-MTAB-9543	yes	32.29
E-HCAD-10	yes	31.37
E-ANND-3	yes	10.95
E-GEOD-135922	yes	8.79
E-CURD-114	yes	7.48
E-MTAB-10290	no	238.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

121 targeting FARP1, 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-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-3910	99.95	71.13	2227

Literature-anchored findings (GeneRIF, showing 4)

• We have reported here for the first time a reduced activity of both Rac1 and Cdc42 in human pheochromocytoma resection as well as tumor-associated expression changes of FARP1, ARHGEF1, and ARHGAP36 (PMID:26911374)
• FARP1 facilitates malignant melanoma cell proliferation and migration by modulating the MAPK signaling pathway. (PMID:31021836)
• FARP1, ARHGEF39, and TIAM2 are essential receptor tyrosine kinase effectors for Rac1-dependent cell motility in human lung adenocarcinoma. (PMID:34731623)
• circFARP1 enables cancer-associated fibroblasts to promote gemcitabine resistance in pancreatic cancer via the LIF/STAT3 axis. (PMID:35045883)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	farp1	ENSDARG00000074381
danio_rerio		ENSDARG00000112056
mus_musculus	Farp1	ENSMUSG00000025555
rattus_norvegicus	Farp1	ENSRNOG00000011203
caenorhabditis_elegans		WBGENE00001366
caenorhabditis_elegans		WBGENE00001490

Paralogs (10): FARP2 (ENSG00000006607), FGD1 (ENSG00000102302), FGD3 (ENSG00000127084), ARHGEF39 (ENSG00000137135), FGD4 (ENSG00000139132), FGD2 (ENSG00000146192), FGD5 (ENSG00000154783), FRMD7 (ENSG00000165694), FGD6 (ENSG00000180263), ECT2L (ENSG00000203734)

Protein

Protein identifiers

FERM, ARHGEF and pleckstrin domain-containing protein 1 — Q9Y4F1 (reviewed: Q9Y4F1)

Alternative names: Chondrocyte-derived ezrin-like protein, FERM, RhoGEF and pleckstrin domain-containing protein 1, Pleckstrin homology domain-containing family C member 2

All UniProt accessions (8): Q9Y4F1, A0A1B0GV68, A0A2X0TVY0, C9JME2, H0Y783, M0QXT1, M0QYB0, M0R262

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a guanine nucleotide exchange factor for RAC1. May play a role in semaphorin signaling. Plays a role in the assembly and disassembly of dendritic filopodia, the formation of dendritic spines, regulation of dendrite length and ultimately the formation of synapses.

Subunit / interactions. Interacts with CADM1. Interacts with RAC1.

Subcellular location. Cell membrane. Synapse. Synaptosome. Cytoplasm. Cytosol. Cell projection. Filopodium. Dendrite. Dendritic spine.

Tissue specificity. Detected in cAMP-treated chondrocytes, but not in untreated chondrocytes. Detected in fetal brain, heart and spleen, and in adult testis, kidney and lung.

Domain organisation. Intramolecular interaction between the DH domain and the PH domains can stabilize the protein in an autoinhibited conformation.

Induction. Up-regulated in response to cAMP in cultured embryonic chondrocytes.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y4F1-1	1	yes
Q9Y4F1-2	2
Q9Y4F1-3	3

RefSeq proteins (3): NP_001001715, NP_001273768, NP_005757* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000219	DH_dom	Domain
IPR000299	FERM_domain	Domain
IPR000798	Ez/rad/moesin-like	Family
IPR001849	PH_domain	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR014352	FERM/acyl-CoA-bd_prot_sf	Homologous_superfamily
IPR014847	FA	Domain
IPR018979	FERM_N	Domain
IPR018980	FERM_PH-like_C	Domain
IPR019747	FERM_CS	Conserved_site
IPR019748	FERM_central	Domain
IPR019749	Band_41_domain	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR035899	DBL_dom_sf	Homologous_superfamily
IPR035963	FERM_2	Homologous_superfamily
IPR041788	FARP1/FARP2/FRMD7_FERM_C	Domain
IPR051835	RAC1-GEF	Family

Pfam: PF00169, PF00373, PF00621, PF08736, PF09379, PF09380

UniProt features (36 total): modified residue 19, domain 4, compositionally biased region 3, splice variant 3, region of interest 3, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4H6Y	X-RAY DIFFRACTION	4.09

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y4F1-F1	77.29	0.60

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 (19): 20, 23, 24, 340, 373, 389, 403, 418, 427, 433, 510, 514, 833, 872, 878, 883, 889, 896, 899

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-8980692	RHOA GTPase cycle
R-HSA-9013148	CDC42 GTPase cycle
R-HSA-9013149	RAC1 GTPase cycle
R-HSA-9035034	RHOF GTPase cycle

MSigDB gene sets: 278 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_DENDRITE_DEVELOPMENT, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, HNF3ALPHA_Q6, GOBP_SYNAPSE_ASSEMBLY, ATACCTC_MIR202, GOZGIT_ESR1_TARGETS_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOMF_GTPASE_BINDING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, USF_C, GOBP_CELL_CELL_SIGNALING

GO Biological Process (8): enzyme-linked receptor protein signaling pathway (GO:0007167), synapse assembly (GO:0007416), Rac protein signal transduction (GO:0016601), dendrite morphogenesis (GO:0048813), retrograde trans-synaptic signaling by trans-synaptic protein complex (GO:0098942), postsynaptic actin cytoskeleton organization (GO:0098974), positive regulation of skeletal muscle acetylcholine-gated channel clustering (GO:1904395), regulation of presynapse assembly (GO:1905606)

GO Molecular Function (4): guanyl-nucleotide exchange factor activity (GO:0005085), cytoskeletal protein binding (GO:0008092), small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (14): cytosol (GO:0005829), cytoskeleton (GO:0005856), cytoplasmic side of plasma membrane (GO:0009898), filopodium (GO:0030175), dendrite (GO:0030425), dendritic spine (GO:0043197), extrinsic component of postsynaptic membrane (GO:0098890), glutamatergic synapse (GO:0098978), cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995), neuron projection (GO:0043005), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RHO GTPase cycle	4

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cell surface receptor signaling pathway	1
nervous system development	1
cell junction assembly	1
synapse organization	1
small GTPase-mediated signal transduction	1
dendrite development	1
cell morphogenesis involved in neuron differentiation	1
neuron projection morphogenesis	1
retrograde trans-synaptic signaling	1
trans-synaptic signaling by trans-synaptic complex	1
actin cytoskeleton organization	1
postsynaptic cytoskeleton organization	1
skeletal muscle acetylcholine-gated channel clustering	1
positive regulation of receptor clustering	1
regulation of skeletal muscle acetylcholine-gated channel clustering	1
regulation of synapse assembly	1
presynapse assembly	1
regulation of presynapse organization	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
protein binding	1
GTPase binding	1
binding	1
cytoplasm	1
intracellular membraneless organelle	1
plasma membrane	1
cytoplasmic side of membrane	1
actin-based cell projection	1
neuron projection	1
dendritic tree	1
dendrite	1
neuron spine	1
postsynapse	1
postsynaptic membrane	1
extrinsic component of synaptic membrane	1
synapse	1
intracellular anatomical structure	1
membrane	1

Protein interactions and networks

STRING

1028 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FARP1	PLEK2	Q9NYT0	696
FARP1	PLEK	P08567	695
FARP1	PLXNA4	Q9HCM2	620
FARP1	RNF113B	Q8IZP6	571
FARP1	SEMA6A	Q9H2E6	559
FARP1	CDC42	P21181	559
FARP1	CADM1	Q9BY67	548
FARP1	PLXND1	Q9Y4D7	483
FARP1	CLSTN3	Q9BQT9	465
FARP1	DOCK9	Q9BZ29	403
FARP1	DCAF12L2	Q5VW00	402
FARP1	MCF2	P10911	395
FARP1	PTEN	P60484	388
FARP1	SDCBP2	Q9H190	388
FARP1	DCAF12L1	Q5VU92	381

IntAct

108 interactions, top by confidence:

A	B	Type	Score
LSM3	LSM1	psi-mi:“MI:0914”(association)	0.950
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
KCNJ2	KCNJ18	psi-mi:“MI:2364”(proximity)	0.660
CAMKV	AP3B1	psi-mi:“MI:0914”(association)	0.640
SDC2	PDPK1	psi-mi:“MI:0914”(association)	0.640
SNRPB	SART1	psi-mi:“MI:0914”(association)	0.640
NS1	PIK3R2	psi-mi:“MI:0914”(association)	0.560
PIH1D1	FARP1	psi-mi:“MI:0915”(physical association)	0.560
PLK1	C1orf226	psi-mi:“MI:0914”(association)	0.560
DCAF8	DCAF8L1	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
HADHA	AGRN	psi-mi:“MI:0914”(association)	0.530
DCAF8	TCP1	psi-mi:“MI:0914”(association)	0.530
LSM4	PRMT5	psi-mi:“MI:0914”(association)	0.530
GAR1	PRMT5	psi-mi:“MI:0914”(association)	0.530
ANK2	ACOT7	psi-mi:“MI:0914”(association)	0.500
FARP1	PPP1CA	psi-mi:“MI:0407”(direct interaction)	0.440
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
Flot1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Flot2	ACTG1	psi-mi:“MI:0914”(association)	0.350
MYO1C	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Prmt5	WIZ	psi-mi:“MI:0914”(association)	0.350

BioGRID (162): FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS), FARP1 (Affinity Capture-MS)

ESM2 similar proteins: A2ALK8, A8XWC4, D3ZDI6, F1LYQ8, F1M386, F1MSG6, F1P065, F1PBJ0, F8VPU2, G5EDB9, O14936, O35239, O70589, O94887, P26045, P28191, P43378, P54936, P70600, P97874, Q05397, Q05AK5, Q14289, Q14644, Q15283, Q28013, Q3UYK3, Q4KWH5, Q4KWH8, Q58CU2, Q5RAB8, Q60790, Q62915, Q641Z2, Q6NVF0, Q6P7F1, Q6TEM9, Q8BM54, Q8CHG7, Q8TEU7

Diamond homologs: A2A2Y4, A2AD83, A2ALK8, B2RYE5, F1LYQ8, F1P065, F8VPU2, O43491, O57457, O70318, O94887, P11171, P11434, P26045, P28191, P29074, P48193, P52963, Q0P4Q4, Q54K81, Q58CU2, Q5FVG2, Q5R803, Q5RAB8, Q6P5H6, Q6Q7P4, Q6ZUT3, Q7Z6J6, Q8BGS1, Q8BHD4, Q91VS8, Q9H329, Q9H4G0, Q9HCM4, Q9HCS5, Q9JMC8, Q9MYU8, Q9N179, Q9V8R9, Q9WTP0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 143 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
Attachment and Entry	5	32.7×	3e-05
Defective B4GALT7 causes EDS, progeroid type	5	31.0×	3e-05
Defective B3GAT3 causes JDSSDHD	5	31.0×	3e-05
Defective B3GALT6 causes EDSP2 and SEMDJL1	5	31.0×	3e-05
HS-GAG degradation	5	27.0×	5e-05
Respiratory syncytial virus (RSV) attachment and entry	5	27.0×	5e-05
Initiation of coagulation cascade	5	25.9×	6e-05
Glycosaminoglycan-protein linkage region biosynthesis	5	21.4×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	7	34.2×	1e-06
RNA splicing	10	7.4×	5e-04
mRNA splicing, via spliceosome	9	6.9×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	222
Likely benign	10
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

6054 predictions. Top by Δscore:

Variant	Effect	Δscore
13:98191274:G:GT	donor_gain	1.0000
13:98213206:ACT:A	acceptor_gain	1.0000
13:98213208:T:A	acceptor_gain	1.0000
13:98213217:CAGAT:C	acceptor_loss	1.0000
13:98213218:A:AG	acceptor_gain	1.0000
13:98213219:G:GG	acceptor_gain	1.0000
13:98213219:GA:G	acceptor_gain	1.0000
13:98213219:GAT:G	acceptor_gain	1.0000
13:98213219:GATA:G	acceptor_gain	1.0000
13:98213396:G:GT	donor_gain	1.0000
13:98213409:TTCCA:T	donor_gain	1.0000
13:98213410:TCCA:T	donor_gain	1.0000
13:98213410:TCCAG:T	donor_loss	1.0000
13:98213413:AG:A	donor_loss	1.0000
13:98213414:G:GG	donor_gain	1.0000
13:98213415:TA:T	donor_loss	1.0000
13:98213416:AA:A	donor_loss	1.0000
13:98343758:ACAG:A	acceptor_loss	1.0000
13:98343759:CAG:C	acceptor_loss	1.0000
13:98343760:A:AG	acceptor_gain	1.0000
13:98343761:G:GA	acceptor_gain	1.0000
13:98343761:GC:G	acceptor_gain	1.0000
13:98343761:GCAA:G	acceptor_gain	1.0000
13:98343761:GCAAA:G	acceptor_gain	1.0000
13:98343865:CGGTA:C	donor_loss	1.0000
13:98343867:G:C	donor_loss	1.0000
13:98343867:G:GG	donor_gain	1.0000
13:98343868:T:A	donor_loss	1.0000
13:98365389:TTCTA:T	acceptor_loss	1.0000
13:98365390:TCTA:T	acceptor_loss	1.0000

AlphaMissense

6925 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:98385750:C:A	A232D	1.000
13:98385780:T:C	L242P	1.000
13:98388410:T:A	W263R	1.000
13:98388410:T:C	W263R	1.000
13:98388412:G:C	W263C	1.000
13:98388412:G:T	W263C	1.000
13:98388425:A:G	K268E	1.000
13:98388431:A:C	S270R	1.000
13:98388433:C:A	S270R	1.000
13:98388433:C:G	S270R	1.000
13:98388434:T:C	F271L	1.000
13:98388435:T:C	F271S	1.000
13:98388436:C:A	F271L	1.000
13:98388436:C:G	F271L	1.000
13:98388450:T:C	F276S	1.000
13:98388453:T:C	L277P	1.000
13:98389982:T:C	F294S	1.000
13:98390006:G:A	C302Y	1.000
13:98390007:C:G	C302W	1.000
13:98390010:G:C	K303N	1.000
13:98390010:G:T	K303N	1.000
13:98390017:T:A	W306R	1.000
13:98390017:T:C	W306R	1.000
13:98390019:G:C	W306C	1.000
13:98390019:G:T	W306C	1.000
13:98390030:T:A	V310D	1.000
13:98390102:G:A	G334E	1.000
13:98439159:T:C	F799S	1.000
13:98440145:T:A	W847R	1.000
13:98440145:T:C	W847R	1.000

dbSNP variants (sampled 300 via entrez): RS1000016556 (13:98231028 C>T), RS1000020273 (13:98147688 T>C), RS1000063631 (13:98362176 A>C), RS1000072840 (13:98225726 G>A,C), RS1000104722 (13:98342895 A>C,T), RS1000124522 (13:98236552 G>A), RS1000140709 (13:98153182 T>TA), RS1000153403 (13:98318586 GC>G), RS1000178502 (13:98311423 T>C), RS1000182411 (13:98199745 A>G), RS1000200975 (13:98355584 C>G,T), RS1000231911 (13:98449599 A>C), RS1000239725 (13:98153763 C>T), RS1000240415 (13:98336719 T>G), RS1000263973 (13:98385907 C>A,G,T)

Disease associations

OMIM: gene MIM:602654 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

23 associations (top):

Study	Trait	p-value
GCST000597_4	Brain structure	1.000000e-06
GCST000766_8	Non-alcoholic fatty liver disease histology (lobular)	2.000000e-06
GCST000892_10	Total ventricular volume (Alzheimer’s disease interaction)	7.000000e-06
GCST001651_34	Response to amphetamines	6.000000e-06
GCST001762_906	Obesity-related traits	5.000000e-06
GCST002595_23	Clozapine-induced agranulocytosis	8.000000e-06
GCST002598_68	Educational attainment	3.000000e-07
GCST003226_21	Pelvic organ prolapse	7.000000e-06
GCST003427_147	Alzheimer disease and age of onset	9.000000e-07
GCST006665_11	Social science traits (pleiotropy) (HIPO component 1)	7.000000e-10
GCST007709_124	General factor of neuroticism	2.000000e-08
GCST008357_21	Mood instability	8.000000e-12
GCST008357_23	Mood instability	1.000000e-12
GCST008595_78	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	8.000000e-10
GCST009084_2	Pneumococcal meningitis x streptococcus pneumoniae antigen allele interaction	4.000000e-08
GCST009523_54	Household income	4.000000e-08
GCST009523_55	Household income	3.000000e-08
GCST009524_234	Household income (MTAG)	6.000000e-17
GCST010866_53	Coronary artery disease	8.000000e-11
GCST011354_37	Bell’s palsy	3.000000e-07
GCST011741_42	LDL cholesterol levels in HIV infection	8.000000e-06
GCST012489_2	Heel bone mineral density x serum urate levels interaction	6.000000e-12
GCST90000514_21	Gastroesophageal reflux disease	2.000000e-11

EFO canonical traits (13, from GWAS)

EFO ID	Trait name
EFO:0003940	physical activity
EFO:0004784	self reported educational attainment
EFO:0004847	age at onset
EFO:0007006	depressive symptom measurement
EFO:0007660	neuroticism measurement
EFO:0007869	wellbeing measurement
EFO:0008475	mood instability measurement
EFO:0004337	intelligence
EFO:0010271	bacterial pathogen genotype measurement
EFO:0009695	household income
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004531	urate measurement
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs58896682	FARP1, STK24		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, increases methylation, affects cotreatment	6
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation, increases mutagenesis	5
bisphenol A	affects expression, affects cotreatment, increases methylation, decreases expression	3
sodium arsenite	affects methylation, decreases expression, increases expression	3
entinostat	affects cotreatment, decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Fulvestrant	affects cotreatment, increases methylation, decreases reaction, increases expression	2
Acetaminophen	decreases expression, increases expression	2
Quercetin	decreases expression, decreases phosphorylation	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
Asbestos, Serpentine	increases methylation, decreases methylation	2
Cadmium Chloride	increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
dicrotophos	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
terbufos	increases methylation	1
trichostatin A	decreases expression	1
arsenite	increases reaction, affects binding	1
1,6-hexamethylene diisocyanate	increases methylation	1
afimoxifene	increases expression, decreases reaction	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	affects methylation	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SN11	HAP1 FARP1 (-) 1	Cancer cell line	Male
CVCL_SN12	HAP1 FARP1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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