FAT3

Summary

FAT3 (FAT atypical cadherin 3, HGNC:23112) is a protein-coding gene on chromosome 11q14.3, encoding Protocadherin Fat 3 (Q8TDW7). May play a role in the interactions between neurites derived from specific subsets of neurons during development.

Predicted to enable calcium ion binding activity. Predicted to be involved in cell-cell adhesion. Predicted to act upstream of or within generation of neurons; negative regulation of dendrite development; and retina layer formation. Predicted to be located in dendrite and plasma membrane.

Source: NCBI Gene 120114 — RefSeq curated summary.

At a glance

• GWAS associations: 29
• Clinical variants (ClinVar): 751 total
• Cancer driver (intOGen): activating (oncogene-like) across 21 cancer types
• MANE Select transcript: NM_001367949

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23112
Approved symbol	FAT3
Name	FAT atypical cadherin 3
Location	11q14.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1989, CDHF15, CDHR10
Ensembl gene	ENSG00000165323
Ensembl biotype	protein_coding
OMIM	612483
Entrez	120114

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000409404, ENST00000469900, ENST00000489716, ENST00000525166, ENST00000528921

RefSeq mRNA: 2 — MANE Select: NM_001367949 NM_001008781, NM_001367949

CCDS: CCDS91573

Canonical transcript exons

ENST00000525166 — 28 exons

Exon	Start	End
ENSE00001092120	92866741	92867209
ENSE00001092121	92859165	92859322
ENSE00001092122	92857214	92857348
ENSE00001092124	92880731	92880884
ENSE00001202429	92882738	92883393
ENSE00001202440	92843934	92844732
ENSE00001202449	92840562	92840759
ENSE00001594171	92837663	92837806
ENSE00001618597	92697384	92697445
ENSE00001629080	92789943	92790218
ENSE00001637579	92774041	92774180
ENSE00001656779	92524634	92524948
ENSE00001671164	92806362	92806515
ENSE00001671223	92834870	92835084
ENSE00001672944	92805153	92805349
ENSE00001680288	92836566	92836703
ENSE00001709176	92352096	92355404
ENSE00001725058	92761856	92762170
ENSE00001753366	92831622	92832011
ENSE00001758505	92809843	92810076
ENSE00001775568	92764879	92765089
ENSE00001802371	92792767	92792977
ENSE00001803295	92797836	92801909
ENSE00002161020	92890491	92896473
ENSE00003665440	92889856	92889891
ENSE00003676106	92889189	92889248
ENSE00003681506	92887000	92887113
ENSE00003913498	92224818	92225174

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 99.10.

FANTOM5 (CAGE): breadth broad, TPM avg 6.1490 / max 281.6441, expressed in 701 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116195	4.2776	585
116191	0.4014	248
116200	0.2982	154
116199	0.2592	125
116194	0.2111	128
116193	0.1571	92
116210	0.1469	67
116197	0.1364	69
116198	0.0981	49
116192	0.0883	41

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	99.10	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.55	gold quality
middle temporal gyrus	UBERON:0002771	97.93	gold quality
endothelial cell	CL:0000115	97.57	gold quality
lateral globus pallidus	UBERON:0002476	96.18	gold quality
cortical plate	UBERON:0005343	96.04	gold quality
tibia	UBERON:0000979	94.97	gold quality
parietal lobe	UBERON:0001872	94.59	gold quality
entorhinal cortex	UBERON:0002728	94.57	gold quality
postcentral gyrus	UBERON:0002581	94.53	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.53	gold quality
Brodmann (1909) area 46	UBERON:0006483	93.58	gold quality
superior frontal gyrus	UBERON:0002661	93.34	gold quality
saphenous vein	UBERON:0007318	93.03	gold quality
seminal vesicle	UBERON:0000998	91.09	gold quality
ventral tegmental area	UBERON:0002691	90.56	gold quality
superior vestibular nucleus	UBERON:0007227	90.27	gold quality
occipital lobe	UBERON:0002021	89.83	gold quality
dorsal plus ventral thalamus	UBERON:0001897	89.18	gold quality
substantia nigra pars reticulata	UBERON:0001966	88.99	gold quality
substantia nigra pars compacta	UBERON:0001965	88.80	gold quality
globus pallidus	UBERON:0001875	88.58	gold quality
primary visual cortex	UBERON:0002436	88.50	gold quality
medial globus pallidus	UBERON:0002477	87.20	gold quality
medulla oblongata	UBERON:0001896	87.02	gold quality
ventricular zone	UBERON:0003053	86.14	gold quality
subthalamic nucleus	UBERON:0001906	85.65	gold quality
nucleus accumbens	UBERON:0001882	84.70	gold quality
ganglionic eminence	UBERON:0004023	84.66	gold quality
inferior vagus X ganglion	UBERON:0005363	82.37	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	92.46
E-HCAD-25	yes	80.14
E-ANND-3	yes	7.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

291 targeting FAT3, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996

Literature-anchored findings (GeneRIF, showing 6)

• For Fat3, the Kif5-ID is regulated by alternative splicing, and the timecourse of splicing suggests that the distribution of Fat3 may switch between early and later stages of retinal development. In contrast, P75NTR binding to Kif5B is enhanced by tyrosine phosphorylation and thus has the potential to be dynamically regulated on a more rapid time scale (PMID:27788242)
• A circular RNA derived from FAT atypical cadherin 3 promotes lung cancer progression via forming a regulatory loop with oncogenic ELAV like RNA binding protein 1. (PMID:34647573)
• Co-Mutation of FAT3 and LRP1B in Lung Adenocarcinoma Defines a Unique Subset Correlated With the Efficacy of Immunotherapy. (PMID:35069585)
• Fat3 acts through independent cytoskeletal effectors to coordinate asymmetric cell behaviors during polarized circuit assembly. (PMID:35108541)
• Identification of FAT3 as a new candidate gene for adolescent idiopathic scoliosis. (PMID:35853984)
• Antitumor immunity and prognosis value elicited by FAT3 and LRP1B co-mutation in endometrial cancer. (PMID:38696842)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	fat3a	ENSDARG00000033840
danio_rerio	fat3b	ENSDARG00000087709
mus_musculus	Fat3	ENSMUSG00000074505
rattus_norvegicus	Fat3	ENSRNOG00000011585
drosophila_melanogaster	stan	FBGN0024836
caenorhabditis_elegans		WBGENE00001475
caenorhabditis_elegans	hmr-1	WBGENE00001980
caenorhabditis_elegans	Y52B11A.11	WBGENE00014914

Paralogs (6): CELSR3 (ENSG00000008300), CELSR1 (ENSG00000075275), FAT1 (ENSG00000083857), FAT2 (ENSG00000086570), CELSR2 (ENSG00000143126), FAT4 (ENSG00000196159)

Protein

Protein identifiers

Protocadherin Fat 3 — Q8TDW7 (reviewed: Q8TDW7)

Alternative names: Cadherin family member 15, FAT tumor suppressor homolog 3

All UniProt accessions (2): E9PQ73, Q8TDW7

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the interactions between neurites derived from specific subsets of neurons during development.

Subcellular location. Membrane.

Tissue specificity. Expressed in ES cells, primitive neuroectoderm, fetal brain, infant brain, adult neural tissues and prostate.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8TDW7-3	1	yes
Q8TDW7-1	3
Q8TDW7-2	2

RefSeq proteins (2): NP_001008781, NP_001354878* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000152	EGF-type_Asp/Asn_hydroxyl_site	PTM
IPR000742	EGF	Domain
IPR001791	Laminin_G	Domain
IPR001881	EGF-like_Ca-bd_dom	Domain
IPR002126	Cadherin-like_dom	Domain
IPR013032	EGF-like_CS	Conserved_site
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR015919	Cadherin-like_sf	Homologous_superfamily
IPR018097	EGF_Ca-bd_CS	Conserved_site
IPR020894	Cadherin_CS	Conserved_site
IPR056286	Cadherin_CELSR1-3_9th	Domain

Pfam: PF00008, PF00028, PF02210, PF12661, PF23592

UniProt features (99 total): domain 38, glycosylation site 26, disulfide bond 13, sequence variant 9, region of interest 3, topological domain 2, compositionally biased region 2, splice variant 2, signal peptide 1, chain 1, transmembrane region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q8TDW7 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

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 (1): 4510

Disulfide bonds (13): 3799–3810, 3804–3822, 3824–3832, 3985–4018, 4025–4036, 4030–4046, 4048–4057, 4064–4075, 4069–4084, 4086–4095, 4102–4113, 4107–4122, 4124–4133

Glycosylation sites (26): 49, 342, 482, 563, 668, 800, 880, 899, 1007, 1368, 1430, 1752, 1945, 1994, 1997, 2209, 2293, 2332, 2468, 3001 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 185 (showing top): GOBP_DENDRITE_DEVELOPMENT, GOBP_NEUROGENESIS, GOBP_NEURAL_RETINA_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_CELL_CELL_ADHESION, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_DENDRITE_DEVELOPMENT, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_NEURON_MIGRATION, GOBP_RETINA_LAYER_FORMATION, GOBP_NEGATIVE_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOCC_NEURON_PROJECTION

GO Biological Process (13): homophilic cell-cell adhesion (GO:0007156), retina layer formation (GO:0010842), dendrite development (GO:0016358), amacrine cell differentiation (GO:0035881), cell-cell adhesion mediated by cadherin (GO:0044331), cell morphogenesis involved in neuron differentiation (GO:0048667), interneuron migration (GO:1904936), negative regulation of dendrite development (GO:2000171), neuron migration (GO:0001764), cell adhesion (GO:0007155), animal organ morphogenesis (GO:0009887), anatomical structure formation involved in morphogenesis (GO:0048646), regulation of plasma membrane bounded cell projection organization (GO:0120035)

GO Molecular Function (1): calcium ion binding (GO:0005509)

GO Cellular Component (5): plasma membrane (GO:0005886), adherens junction (GO:0005912), dendrite (GO:0030425), membrane (GO:0016020), neuron projection (GO:0043005)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell-cell adhesion	2
neural retina development	2
anatomical structure morphogenesis	2
anatomical structure formation involved in morphogenesis	1
retina morphogenesis in camera-type eye	1
neuron projection development	1
anatomical structure development	1
central nervous system neuron differentiation	1
cell morphogenesis	1
neuron differentiation	1
neuron development	1
neuron migration	1
negative regulation of neuron projection development	1
dendrite development	1
regulation of dendrite development	1
negative regulation of developmental process	1
cell migration	1
generation of neurons	1
cellular process	1
animal organ development	1
developmental process	1
regulation of cell projection organization	1
plasma membrane bounded cell projection organization	1
metal ion binding	1
membrane	1
cell periphery	1
cell-cell junction	1
neuron projection	1
dendritic tree	1
cellular anatomical structure	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

1426 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FAT3	MTNR1B	P49286	828
FAT3	MTNR1A	P48039	804
FAT3	FJX1	Q86VR8	669
FAT3	CSMD3	Q7Z407	668
FAT3	LAMC1	P11047	653
FAT3	LAMA1	P25391	592
FAT3	GABRA6	Q16445	585
FAT3	VASP	P50552	550
FAT3	ZFHX4	Q86UP3	545
FAT3	MUC16	Q8WXI7	544
FAT3	CTNNB1	P35222	515
FAT3	PCLO	Q9Y6V0	509
FAT3	EGF	P01133	506
FAT3	USH2A	O75445	487
FAT3	SPTA1	P02549	478

IntAct

152 interactions, top by confidence:

A	B	Type	Score
COMMD2	CCDC22	psi-mi:“MI:0914”(association)	0.930
SOCS7	NCK2	psi-mi:“MI:0914”(association)	0.670
LGALS1	PODXL	psi-mi:“MI:0914”(association)	0.530
XAGE1A	THAP12	psi-mi:“MI:0914”(association)	0.530
PDGFB	DKC1	psi-mi:“MI:0914”(association)	0.530
DCDC2B	HSPA8	psi-mi:“MI:0914”(association)	0.530
PPIAL4G	ACTB	psi-mi:“MI:0914”(association)	0.530
PER3	PER1	psi-mi:“MI:0914”(association)	0.500
FAT3	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
MAST1	FAT3	psi-mi:“MI:0407”(direct interaction)	0.440
MAGI2	FAT3	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	PDZK1	psi-mi:“MI:0407”(direct interaction)	0.440
DLG3	FAT3	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
SNX27	FAT3	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	RHPN1	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	RADIL	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	ARHGEF11	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.440
PTPN3	FAT3	psi-mi:“MI:0407”(direct interaction)	0.440
PDZD7	FAT3	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440
FAT3	SYNJ2BP	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (82): FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS), FAT3 (Affinity Capture-MS)

ESM2 similar proteins: E9Q7P9, O88277, O93319, P55280, P55281, P55285, P55289, P70408, P79995, P97326, Q08DJ5, Q12864, Q13634, Q14517, Q24298, Q2PZL6, Q3SWX5, Q5DWV1, Q5DWV2, Q5F226, Q63315, Q6B3P0, Q6KEQ9, Q6V0I7, Q6WXV7, Q6WYY1, Q6X862, Q6ZTQ4, Q71M42, Q8BIZ0, Q8BL00, Q8BM92, Q8BNA6, Q8N6Y1, Q8QGH3, Q8R508, Q8TDW7, Q90762, Q90763, Q91838

Diamond homologs: G5ED46, P33450, Q8TDW7, Q90Z37, Q9VAF5, B0KW95, B2KI42, B4USZ0, F1PAA9, O02840, O15943, O35161, O54800, O88277, O88278, O93319, P08641, P09803, P10288, P12830, P15116, P19022, P19534, P20310, P24503, P30944, P33145, P33146, P33147, P33150, P33151, P39038, P55280, P55283, P55284, P55285, P55286, P55287, P55288, P55289

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 151 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
Ras activation upon Ca2+ influx through NMDA receptor	5	30.7×	7e-05
Assembly and cell surface presentation of NMDA receptors	11	30.0×	3e-11
Unblocking of NMDA receptors, glutamate binding and activation	5	29.2×	7e-05
Negative regulation of NMDA receptor-mediated neuronal transmission	5	29.2×	7e-05
Dopamine Neurotransmitter Release Cycle	5	26.7×	9e-05
Long-term potentiation	5	25.6×	9e-05
Neurexins and neuroligins	10	21.2×	8e-09
Protein-protein interactions at synapses	6	17.1×	9e-05

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	47.0×	2e-13
receptor clustering	7	32.1×	5e-07
protein localization to synapse	5	28.2×	8e-05
regulation of postsynaptic membrane neurotransmitter receptor levels	7	25.5×	2e-06
establishment of protein localization	6	19.1×	8e-05
establishment of cell polarity	6	16.9×	1e-04
cell-cell adhesion	12	9.0×	2e-06
protein-containing complex assembly	9	7.5×	3e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 21 cancer types — ANGS, BRCA, CCRCC, CHOL, CLLSLL, COAD, COADREAD, DLBCLNOS, HNSC, LUSC, MEL, NETNOS…(+9 more).

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	604
Likely benign	79
Benign	41

Top pathogenic / likely-pathogenic (0)

SpliceAI

3255 predictions. Top by Δscore:

Variant	Effect	Δscore
11:92355400:GAGTG:G	donor_gain	1.0000
11:92355401:AGTGG:A	donor_loss	1.0000
11:92355402:GTG:G	donor_gain	1.0000
11:92355403:TGGTA:T	donor_loss	1.0000
11:92355405:G:GC	donor_loss	1.0000
11:92355405:G:GG	donor_gain	1.0000
11:92355406:T:G	donor_loss	1.0000
11:92501098:G:GT	donor_gain	1.0000
11:92524630:TCA:T	acceptor_loss	1.0000
11:92524631:CAGG:C	acceptor_loss	1.0000
11:92524632:A:AG	acceptor_gain	1.0000
11:92524632:A:C	acceptor_loss	1.0000
11:92524632:AG:A	acceptor_gain	1.0000
11:92524632:AGG:A	acceptor_gain	1.0000
11:92524632:AGGG:A	acceptor_gain	1.0000
11:92524633:G:GA	acceptor_gain	1.0000
11:92524633:GG:G	acceptor_gain	1.0000
11:92524633:GGG:G	acceptor_gain	1.0000
11:92524633:GGGG:G	acceptor_gain	1.0000
11:92524633:GGGGT:G	acceptor_gain	1.0000
11:92524946:CAGGT:C	donor_loss	1.0000
11:92524947:AGG:A	donor_loss	1.0000
11:92524949:G:T	donor_loss	1.0000
11:92524950:T:G	donor_loss	1.0000
11:92697444:AGG:A	donor_loss	1.0000
11:92697446:GTAA:G	donor_loss	1.0000
11:92697447:T:G	donor_loss	1.0000
11:92355403:TG:T	donor_gain	0.9900
11:92355404:GG:G	donor_gain	0.9900
11:92524626:T:A	acceptor_gain	0.9900

AlphaMissense

30387 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:92352567:A:T	N152I	1.000
11:92352568:T:A	N152K	1.000
11:92352568:T:G	N152K	1.000
11:92352573:T:C	L154P	1.000
11:92352579:C:A	P156H	1.000
11:92352579:C:G	P156R	1.000
11:92352657:C:A	A182E	1.000
11:92762124:T:A	V1313D	1.000
11:92762166:T:C	L1327P	1.000
11:92764928:T:C	L1345P	1.000
11:92764939:T:A	W1349R	1.000
11:92764939:T:C	W1349R	1.000
11:92352273:A:T	E54V	0.999
11:92352274:G:C	E54D	0.999
11:92352274:G:T	E54D	0.999
11:92352426:T:C	L105P	0.999
11:92352468:G:C	R119T	0.999
11:92352468:G:T	R119M	0.999
11:92352469:G:C	R119S	0.999
11:92352469:G:T	R119S	0.999
11:92352471:A:C	E120A	0.999
11:92352471:A:T	E120V	0.999
11:92352555:T:A	V148D	0.999
11:92352560:G:C	D150H	0.999
11:92352561:A:T	D150V	0.999
11:92352570:A:C	D153A	0.999
11:92352578:C:A	P156T	0.999
11:92352578:C:T	P156S	0.999
11:92352584:T:C	F158L	0.999
11:92352585:T:C	F158S	0.999

dbSNP variants (sampled 300 via entrez): RS1000005156 (11:92787727 T>C), RS1000007873 (11:92283883 G>A,T), RS1000009830 (11:92415532 G>A,T), RS1000015124 (11:92286356 G>A), RS1000019556 (11:92240578 A>C), RS1000023478 (11:92879507 C>A,G), RS1000029235 (11:92513772 A>G), RS1000029390 (11:92279773 C>G), RS1000032147 (11:92690922 C>T), RS1000034594 (11:92491370 C>T), RS1000047005 (11:92368985 G>T), RS1000051997 (11:92588922 C>G,T), RS1000059401 (11:92238567 G>T), RS1000060999 (11:92614585 C>T), RS1000068526 (11:92425271 A>T)

Disease associations

OMIM: gene MIM:612483 | disease phenotypes: MIM:142623, MIM:607174

GenCC curated gene-disease

Mondo (2): Hirschsprung disease, susceptibility to, 1 (MONDO:0007723), familial meningioma (MONDO:0011789)

Orphanet (2): Hirschsprung disease (Orphanet:388), Familial multiple meningioma (Orphanet:263662)

HPO phenotypes

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

GWAS associations

29 associations (top):

Study	Trait	p-value
GCST002251_10	Homeostasis model assessment of beta-cell function (dietary factor interaction)	1.000000e-06
GCST002337_46	Amyotrophic lateral sclerosis (sporadic)	8.000000e-06
GCST002726_41	Glucose homeostasis traits	5.000000e-12
GCST002756_5	Subcortical brain region volumes	6.000000e-09
GCST003815_52	Late-onset Alzheimer’s disease	9.000000e-06
GCST003992_23	Photic sneeze reflex	3.000000e-08
GCST005151_1	Colorectal adenoma (advanced)	4.000000e-07
GCST005153_1	Colorectal adenoma (advanced)	2.000000e-06
GCST005577_1	Change in glucose in response to thiazide diuretic treatment in hypertension	2.000000e-08
GCST006979_415	Heel bone mineral density	8.000000e-11
GCST006979_416	Heel bone mineral density	2.000000e-19
GCST007272_32	Pulse pressure	4.000000e-28
GCST008163_67	Height	6.000000e-06
GCST008595_102	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	2.000000e-08
GCST009266_13	Dental caries (decayed and filled deciduous tooth surfaces)	1.000000e-06
GCST009269_12	Dental caries (decayed and filled deciduous teeth)	4.000000e-06
GCST009404_7	Optic cup area	2.000000e-08
GCST009596_3	Osteoarthritis of the hand	3.000000e-06
GCST009958_3	Retinal detachment	5.000000e-08
GCST009959_20	Retinal detachment or retinal break	1.000000e-16
GCST009960_1	Retinal detachment or retinal break	2.000000e-17
GCST009961_1	Retinal detachment with retinal break	6.000000e-06
GCST010002_245	Refractive error	3.000000e-10
GCST010377_2	Retinal detachment	1.000000e-15
GCST010397_19	Gut microbiota (bacterial taxa, rank normal transformation method)	1.000000e-06
GCST010703_282	Brain morphology (MOSTest)	3.000000e-15
GCST010917_8	Proportion of activated microglia (midfrontal cortex)	3.000000e-07
GCST012008_5	Lateral thalamic nuclei volume	6.000000e-09
GCST012245_1	Periodontitis (stage III/IV grade C)	9.000000e-07

EFO canonical traits (15, from GWAS)

EFO ID	Trait name
EFO:0004469	HOMA-B
EFO:0008111	diet measurement
EFO:0006831	acute insulin response measurement
EFO:0004830	caudate nucleus volume
EFO:1001870	late-onset Alzheimers disease
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0004468	glucose measurement
EFO:0009270	heel bone mineral density
EFO:0005763	pulse pressure measurement
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0010698	retinal break
EFO:0007874	gut microbiome measurement
EFO:0004346	neuroimaging measurement
EFO:0006935	thalamus volume

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537443	Meningioma, familial (supp.)

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
rs12786200	FAT3		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, increases expression, affects expression	5
sodium arsenite	decreases expression, affects methylation	3
Tobacco Smoke Pollution	affects expression, decreases expression, increases expression	3
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Nickel	decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
methyleugenol	decreases expression	1
bisphenol A	increases methylation	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	increases expression, affects cotreatment, decreases expression	1
jinfukang	decreases expression, affects cotreatment	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic	increases expression	1
Aspirin	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Doxorubicin	increases expression	1
Estradiol	affects expression	1
Formaldehyde	increases expression	1
Ivermectin	decreases expression	1
Methotrexate	decreases expression	1
N-Nitrosopyrrolidine	increases expression	1
Silicon Dioxide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A1SK	TOV-2881EP	Cancer cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02343562	PHASE4	UNKNOWN	Probiotics for Prophylaxis of Postoperative Hirschsprungs Associated Enterocolitis
NCT07186647	PHASE4	COMPLETED	Laparoscopic-Assisted Transanal Pull-Through for Hirschsprung Disease in Pediatric:Short and Intermediate Outcomes of Two Different Techniques
NCT04081701	PHASE4	RECRUITING	68-Ga DOTATATE PET/MRI in the Diagnosis and Management of Somatostatin Receptor Positive CNS Tumors.
NCT04386642	PHASE4	UNKNOWN	Tranexamic Acid Reduce Blood Loss in Meningioma Resection
NCT06377371	PHASE4	RECRUITING	Feasibility of Intraoperative Tracing of Meningioma Using [Cu64]DOTATATE
NCT04904081	PHASE3	UNKNOWN	Feasibility of Use of Indocyanine Green in Pediatric Colorectal Surgery
NCT00517959	PHASE3	UNKNOWN	SCRT Versus Conventional RT in Children and Young Adults With Low Grade and Benign Brain Tumors
NCT01655927	PHASE3	UNKNOWN	Efficacy of Tranexamic Acid in Brain Tumor Resections
NCT03015701	PHASE3	COMPLETED	S9005 Mifepristone in Meningioma
NCT03558516	PHASE3	COMPLETED	Magnesium and Intraoperative Blood Loss in Meningioma Surgery
NCT04305470	PHASE3	COMPLETED	Gleolan for Visualization of Newly Diagnosed or Recurrent Meningioma
NCT00630838	PHASE2	COMPLETED	Probiotic Prophylaxis of Hirschprung’s Disease Associated Enterocolitis (HAEC)
NCT00003483	PHASE2	TERMINATED	Antineoplaston Therapy in Treating Patients With Meningioma
NCT00589784	PHASE2	COMPLETED	Phase II Trial of Sunitinib (SU011248) in Patients With Recurrent or Inoperable Meningioma
NCT00706810	PHASE2	COMPLETED	Combination of Hydroxyurea and Verapamil for Refractory Meningiomas
NCT00859040	PHASE2	COMPLETED	Monthly SOM230C for Recurrent or Progressive Meningioma
NCT01967823	PHASE2	COMPLETED	T Cell Receptor Immunotherapy Targeting NY-ESO-1 for Patients With NY-ESO-1 Expressing Cancer
NCT02523014	PHASE2	RECRUITING	Vismodegib, FAK Inhibitor GSK2256098, Capivasertib, and Abemaciclib in Treating Patients With Progressive Meningiomas
NCT02648997	PHASE2	ACTIVE_NOT_RECRUITING	An Open-Label Phase II Study of Nivolumab or Nivolumab/Ipilimumab in Adult Participants With Progessive/ Recurrent Meningioma
NCT02831257	PHASE2	COMPLETED	AZD2014 In NF2 Patients With Progressive or Symptomatic Meningiomas
NCT02847559	PHASE2	RECRUITING	Optune Delivered Electric Field Therapy and Bevacizumab in Treating Patients With Recurrent or Progressive Grade 2 or 3 Meningioma
NCT03013387	PHASE2	WITHDRAWN	Dosimetry Guided PRRT With 90Y-DOTATOC
NCT03071874	PHASE2	UNKNOWN	Vistusertib (AZD2014) For Recurrent Grade II-III Meningiomas
NCT03095248	PHASE2	TERMINATED	Trial of Selumetinib in Patients With Neurofibromatosis Type II Related Tumors
NCT03273712	PHASE2	COMPLETED	Dosimetry-Guided, Peptide Receptor Radiotherapy (PRRT) With 90Y-DOTA- tyr3-Octreotide (90Y-DOTATOC)
NCT03971461	PHASE2	ACTIVE_NOT_RECRUITING	Phase II Study of 177Lu-DOTATATE Radionuclide in Adults With Progressive or High-risk Meningioma
NCT04082520	PHASE2	RECRUITING	Lutathera for the Treatment of Inoperable, Progressive Meningioma After External Beam Radiation Therapy
NCT04298541	PHASE2	NOT_YET_RECRUITING	Direct Comparison of Ga-68-DOTATATE and Ga-68-DOTATOC
NCT04374305	PHASE2	RECRUITING	Innovative Trial for Understanding the Impact of Targeted Therapies in NF2-Related Schwannomatosis (INTUITT-NF2)
NCT04659811	PHASE2	ACTIVE_NOT_RECRUITING	Stereotactic Radiosurgery and Immunotherapy (Pembrolizumab) for the Treatment of Recurrent Meningioma
NCT05425004	PHASE2	RECRUITING	Cabozantinib for Patients With Recurrent or Progressive Meningioma
NCT05940493	PHASE2	RECRUITING	Abemaciclib in Newly Diagnosed Meningioma Patients
NCT06012929	PHASE2	WITHDRAWN	A Study of ONC201 for Refractory Meningioma
NCT06126588	PHASE2	RECRUITING	Combination of Everolimus and 177Lu-DOTATATE in the Treatment of Grades 2 and 3 Refractory Meningioma: a Phase IIb Clinical Trial
NCT06132685	PHASE2	RECRUITING	Post-Operative Dosing of Dexamethasone in Patients With Brain Tumors After a Craniotomy, PODS Trial
NCT06322342	PHASE2	COMPLETED	Phase 2 Ascending Dose Safety and Efficacy Study of RVP-001, a Manganese-based MRI Contrast Agent
NCT06326190	PHASE2	RECRUITING	177Lu-DOTATATE for Recurrent Meningioma
NCT06439420	PHASE2	COMPLETED	CBT-I in Primary Brain Tumor Patients: Phase IIc Randomized Feasibility Pilot Trial
NCT06684795	PHASE2	RECRUITING	FG001 in Subjects with Meningiomas or Presumed Low-Grade Gliomas Scheduled for Neurosurgery
NCT06710249	PHASE2	RECRUITING	Impact of Salovum® and SPC® Flakes on Brain Tumor Induced Edema