CSMD3

Summary

CSMD3 (CUB and Sushi multiple domains 3, HGNC:19291) is a protein-coding gene on chromosome 8q23.3, encoding CUB and sushi domain-containing protein 3 (Q7Z407). Involved in dendrite development.

Predicted to be involved in regulation of dendrite development. Predicted to be located in plasma membrane.

Source: NCBI Gene 114788 — RefSeq curated summary.

At a glance

• Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC)
• GWAS associations: 21
• Clinical variants (ClinVar): 575 total
• Phenotypes (HPO): 1
• Cancer driver (intOGen): activating (oncogene-like) across 18 cancer types
• MANE Select transcript: NM_198123

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19291
Approved symbol	CSMD3
Name	CUB and Sushi multiple domains 3
Location	8q23.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000164796
Ensembl biotype	protein_coding
OMIM	608399
Entrez	114788

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 retained_intron, 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000297405, ENST00000339701, ENST00000343508, ENST00000455883, ENST00000462254, ENST00000492692, ENST00000493303, ENST00000497026, ENST00000519485, ENST00000534172

RefSeq mRNA: 4 — MANE Select: NM_198123 NM_001363185, NM_052900, NM_198123, NM_198124

CCDS: CCDS6315, CCDS6316, CCDS6317

Canonical transcript exons

ENST00000297405 — 71 exons

Exon	Start	End
ENSE00001087542	112255254	112255427
ENSE00001087557	112263639	112263812
ENSE00001087561	112265411	112265590
ENSE00001087586	112337543	112337731
ENSE00001087593	112383567	112383663
ENSE00001087598	112390664	112390788
ENSE00001087599	112346097	112346213
ENSE00001087603	112472591	112472707
ENSE00001087609	112408318	112408413
ENSE00001201268	112287064	112287246
ENSE00001201313	112281174	112281350
ENSE00001291336	112406524	112406727
ENSE00001292210	112408919	112409032
ENSE00001295519	112506691	112506829
ENSE00001298292	112636817	112637005
ENSE00001298881	112352416	112352534
ENSE00001304025	112492489	112492683
ENSE00001306738	112550671	112550873
ENSE00001307820	112556763	112556954
ENSE00001310683	112638696	112638911
ENSE00001313565	112351175	112351244
ENSE00001315308	112517034	112517225
ENSE00001319430	112587066	112587235
ENSE00001320189	112380352	112380456
ENSE00001324568	112503790	112503977
ENSE00001327720	112552594	112552720
ENSE00001328227	112573501	112573657
ENSE00001338519	112289365	112289538
ENSE00001338520	112291510	112291695
ENSE00001338521	112292537	112292710
ENSE00001338522	112295833	112296006
ENSE00001338524	112301793	112301966
ENSE00001338526	112306007	112306192
ENSE00001338528	112310978	112311166
ENSE00001338535	112341477	112341686
ENSE00001338799	112645109	112645225
ENSE00001338801	112650161	112650349
ENSE00001338804	112656154	112656341
ENSE00001338807	112682442	112682636
ENSE00001338810	112685406	112685732
ENSE00001338813	112689868	112690050
ENSE00001338816	112800162	112800274
ENSE00001338818	112829686	112829789
ENSE00001338821	112859145	112859266
ENSE00001338822	112921627	112921751
ENSE00001340488	112947790	112947877
ENSE00001340489	112954684	112954761
ENSE00001340490	113019067	113019179
ENSE00001374942	112304721	112304915
ENSE00001382041	112975837	112976148
ENSE00001654237	112666277	112666415
ENSE00001850376	113436677	113436939
ENSE00001924906	112222928	112224930
ENSE00003468583	112335329	112335474
ENSE00003508574	112231545	112231632
ENSE00003520668	112228756	112228891
ENSE00003523375	112237190	112237348
ENSE00003525796	113098756	113098963
ENSE00003541532	113314571	113314793
ENSE00003593652	113173722	113173916
ENSE00003593844	112318837	112318950
ENSE00003603374	112314429	112314617
ENSE00003609061	112319901	112319981
ENSE00003612710	112247020	112247131
ENSE00003615817	112241720	112241785
ENSE00003625104	112336652	112336829
ENSE00003676836	112254253	112254326
ENSE00003677698	113278592	113278704
ENSE00003679078	112313906	112314052
ENSE00003684193	112234365	112234477
ENSE00003686676	112244394	112244573

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 91.63.

FANTOM5 (CAGE): breadth broad, TPM avg 7.0337 / max 1464.0687, expressed in 329 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
94459	6.5164	309
94461	0.2191	88
94457	0.0644	17
94465	0.0590	2
94462	0.0553	16
94463	0.0527	12
94460	0.0431	20
94455	0.0193	10
94464	0.0044	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	91.63	gold quality
Brodmann (1909) area 23	UBERON:0013554	89.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.78	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.63	gold quality
secondary oocyte	CL:0000655	81.58	gold quality
cortical plate	UBERON:0005343	80.38	gold quality
primary visual cortex	UBERON:0002436	80.13	gold quality
endothelial cell	CL:0000115	78.63	silver quality
superior frontal gyrus	UBERON:0002661	75.28	gold quality
entorhinal cortex	UBERON:0002728	74.92	gold quality
occipital lobe	UBERON:0002021	74.52	gold quality
prefrontal cortex	UBERON:0000451	74.22	gold quality
corpus callosum	UBERON:0002336	72.99	gold quality
hypothalamus	UBERON:0001898	72.73	gold quality
temporal lobe	UBERON:0001871	72.65	gold quality
nucleus accumbens	UBERON:0001882	72.63	gold quality
neocortex	UBERON:0001950	72.40	gold quality
frontal cortex	UBERON:0001870	72.38	gold quality
cerebral cortex	UBERON:0000956	72.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.28	gold quality
postcentral gyrus	UBERON:0002581	71.96	gold quality
Ammon’s horn	UBERON:0001954	71.68	gold quality
Brodmann (1909) area 46	UBERON:0006483	71.47	gold quality
amygdala	UBERON:0001876	71.46	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.11	gold quality
anterior cingulate cortex	UBERON:0009835	70.55	gold quality
caudate nucleus	UBERON:0001873	69.90	gold quality
parietal lobe	UBERON:0001872	69.88	gold quality
forebrain	UBERON:0001890	68.86	gold quality
right frontal lobe	UBERON:0002810	68.79	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	76.85
E-HCAD-25	yes	19.28
E-ANND-3	yes	8.52
E-ENAD-17	no	77.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

213 targeting CSMD3, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5692A	100.00	74.40	6850
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-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
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-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939

Literature-anchored findings (GeneRIF, showing 6)

• CSMD3 protein domain structure and the sequence of the cytoplasmic tail are highly conserved between mammals and fish. (PMID:12906867)
• CSMD3 encodes a protein with CUB and sushi multiple domains and is a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1 (PMID:12943675)
• CSMD3 is deleted in a subject with combined tricho-rhino-phalangeal syndrome II with mental retardation and growth hormone deficiency. (PMID:15523607)
• Breakpoints on chromosomes 8 in both patients do not interrupt any known gene but both map in a region containing the CSMD3 gene, which thereby can be considered as a candidate for autistic spectrum disorders (PMID:18270536)
• Single-nucleotide polymorphisms in CSMD3 is associated with prostate cancer risk in hispanic men. (PMID:19528667)
• Nonsynonymous variants of CSMD3 is associated with familial colorectal cancer. (PMID:21351276)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	csmd3a	ENSDARG00000077905
danio_rerio	csmd3b	ENSDARG00000077920
mus_musculus	Csmd3	ENSMUSG00000022311
rattus_norvegicus	Csmd3	ENSRNOG00000004937

Paralogs (39): CFH (ENSG00000000971), SELE (ENSG00000007908), C8B (ENSG00000021852), C6 (ENSG00000039537), SEZ6 (ENSG00000063015), CFHR2 (ENSG00000080910), APOH (ENSG00000091583), SEZ6L (ENSG00000100095), SUSD6 (ENSG00000100647), SRPX (ENSG00000101955), SRPX2 (ENSG00000102359), C7 (ENSG00000112936), C9 (ENSG00000113600), PAPPA2 (ENSG00000116183), CFHR3 (ENSG00000116785), CR2 (ENSG00000117322), CD46 (ENSG00000117335), CSMD2 (ENSG00000121904), C4BPA (ENSG00000123838), C4BPB (ENSG00000123843), CFHR4 (ENSG00000134365), CFHR5 (ENSG00000134389), F13B (ENSG00000143278), SUSD4 (ENSG00000143502), C8A (ENSG00000157131), SUSD3 (ENSG00000157303), SVEP1 (ENSG00000165124), C2 (ENSG00000166278), SELP (ENSG00000174175), SEZ6L2 (ENSG00000174938), PRF1 (ENSG00000180644), PAPPA (ENSG00000182752), CSMD1 (ENSG00000183117), SELL (ENSG00000188404), CD55 (ENSG00000196352), CR1L (ENSG00000197721), CR1 (ENSG00000203710), CFB (ENSG00000243649), CFHR1 (ENSG00000244414)

Protein

Protein identifiers

CUB and sushi domain-containing protein 3 — Q7Z407 (reviewed: Q7Z407)

Alternative names: CUB and sushi multiple domains protein 3

All UniProt accessions (2): Q7Z407, H7BXX0

UniProt curated annotations — full annotation on UniProt →

Function. Involved in dendrite development.

Subcellular location. Cell membrane.

Tissue specificity. Weakly expressed in most tissues, except in brain. Expressed at intermediate level in brain, including cerebellum, substantia nigra, thalamus, spinal cord, hippocampus and fetal brain. Also expressed in testis.

Domain organisation. The intracellular region is dispensable for its function.

Similarity. Belongs to the CSMD family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q7Z407-1	1	yes
Q7Z407-2	2
Q7Z407-3	3
Q7Z407-4	4
Q7Z407-5	5

RefSeq proteins (4): NP_001350114, NP_443132, NP_937756, NP_937757 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000436	Sushi_SCR_CCP_dom	Domain
IPR000859	CUB_dom	Domain
IPR035914	Sperma_CUB_dom_sf	Homologous_superfamily
IPR035976	Sushi/SCR/CCP_sf	Homologous_superfamily
IPR051277	SEZ6_CSMD_C4BPB_Regulators	Family

Pfam: PF00084, PF00431

UniProt features (179 total): disulfide bond 70, domain 42, glycosylation site 41, sequence variant 7, splice variant 6, sequence conflict 4, topological domain 3, transmembrane region 2, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

No AlphaFold model available for Q7Z407 — 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.

Disulfide bonds (70): 690–717, 721–747, 834–875, 860–891, 895–921, 1010–1050, 1036–1063, 1067–1093, 1182–1222, 1208–1237, 1241–1267, 1354–1395, 1381–1410, 1414–1441, 1528–1568, 1554–1584, 1588–1614, 1701–1741, 1727–1758, 1762–1788 …

Glycosylation sites (41): 73, 90, 361, 409, 724, 823, 966, 1092, 1126, 1171, 1280, 1536, 1591, 1709, 1781, 1929, 2019, 2155, 2286, 2291 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 200 (showing top): GOBP_DENDRITE_DEVELOPMENT, RNGTGGGC_UNKNOWN, RRAGTTGT_UNKNOWN, AP1_01, BENPORATH_ES_WITH_H3K27ME3, GCANCTGNY_MYOD_Q6, AREB6_01, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, FOXO4_01, CAGCTG_AP4_Q5, ATGTTAA_MIR302C, EVI1_05, CCANNAGRKGGC_UNKNOWN, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION

GO Biological Process (1): regulation of dendrite development (GO:0050773)

GO Molecular Function (0):

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of neuron projection development	1
dendrite development	1
regulation of developmental process	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1256 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSMD3	TRPS1	Q9UHF7	852
CSMD3	ANXA13	P27216	833
CSMD3	LRP1B	Q9NZR2	767
CSMD3	MUC16	Q8WXI7	720
CSMD3	EXT1	Q16394	708
CSMD3	TTN	Q8WZ42	707
CSMD3	FAT3	Q8TDW7	668
CSMD3	SYNE1	Q8NF91	667
CSMD3	PCLO	Q9Y6V0	663
CSMD3	ZFHX4	Q86UP3	658
CSMD3	USH2A	O75445	643
CSMD3	GDF6	Q6KF10	638
CSMD3	RYR2	Q92736	608
CSMD3	XIRP2	A4UGR9	605
CSMD3	PKHD1L1	Q86WI1	585

IntAct

2 interactions, top by confidence:

A	B	Type	Score
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): CSMD3 (Proximity Label-MS), CSMD3 (Affinity Capture-MS), CSMD3 (Positive Genetic), CSMD3 (Co-fractionation), CSMD3 (Co-fractionation), CSMD3 (Co-fractionation)

ESM2 similar proteins: A0A1D5NSM8, A2AVA0, B8JI71, D3ZHH1, F1RWC3, O57409, O60494, O70244, O75445, P0C6B8, P25723, P35442, P56677, P82279, P86091, P97435, P98072, P98073, P98074, P98160, Q05793, Q0IIH7, Q16787, Q20176, Q2QI47, Q4LDE5, Q5ZQU0, Q61789, Q66TN7, Q70E20, Q7RTY8, Q7RTZ1, Q7Z407, Q7Z408, Q80T79, Q8BIK6, Q8K3K1, Q8K480, Q8UWJ4, Q8VHS2

Diamond homologs: A8WCC4, F1RWC3, O35276, O35375, O43897, O57382, O57460, O60462, O60494, O70244, P13497, P25723, P98063, P98070, Q20176, Q5RA73, Q62381, Q6V9H4, Q7Z407, Q7Z408, Q80T79, Q8CI19, Q8JI28, Q8QFX6, Q925I7, Q9DER7, Q9EQT1, Q9EQX6, Q9GZP0, Q9I946, Q9JLB4, Q9NRA1, Q9TU53, Q9VC47, Q9W332, Q9WVM6, Q9Y6L7, A0JNA2, B3EWZ7, B3EX01

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 18 cancer types — BLCA, BRCA, COAD, COADREAD, ESCA, GBM, HCC, HNSC, LUAD, LUSC, MEL, OVT…(+6 more).

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	454
Likely benign	47
Benign	42

Top pathogenic / likely-pathogenic (0)

SpliceAI

11735 predictions. Top by Δscore:

Variant	Effect	Δscore
8:112231540:ATTAC:A	donor_loss	1.0000
8:112231542:TACCC:T	donor_loss	1.0000
8:112231543:A:AC	donor_gain	1.0000
8:112231543:A:G	donor_loss	1.0000
8:112231543:AC:A	donor_gain	1.0000
8:112231544:C:CC	donor_gain	1.0000
8:112231544:CC:C	donor_gain	1.0000
8:112231633:C:CA	acceptor_loss	1.0000
8:112231634:T:C	acceptor_loss	1.0000
8:112234357:ATACT:A	donor_loss	1.0000
8:112234358:TACTT:T	donor_loss	1.0000
8:112234359:A:AC	donor_gain	1.0000
8:112234359:ACTT:A	donor_loss	1.0000
8:112234360:C:CC	donor_gain	1.0000
8:112234360:CT:C	donor_loss	1.0000
8:112234361:TTAC:T	donor_loss	1.0000
8:112234362:TACAA:T	donor_loss	1.0000
8:112234363:A:AC	donor_gain	1.0000
8:112234364:C:CG	donor_gain	1.0000
8:112234364:CA:C	donor_gain	1.0000
8:112234364:CAA:C	donor_gain	1.0000
8:112234364:CAAA:C	donor_gain	1.0000
8:112234364:CAAAG:C	donor_gain	1.0000
8:112234390:T:TA	donor_gain	1.0000
8:112234473:TACCC:T	acceptor_gain	1.0000
8:112234475:CCC:C	acceptor_gain	1.0000
8:112234476:CC:C	acceptor_gain	1.0000
8:112234476:CCC:C	acceptor_gain	1.0000
8:112234477:CC:C	acceptor_gain	1.0000
8:112234478:C:CC	acceptor_gain	1.0000

AlphaMissense

24333 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:112228798:G:T	A3641E	1.000
8:112228807:G:C	P3638R	1.000
8:112228807:G:T	P3638H	1.000
8:112237316:A:G	W3501R	1.000
8:112237316:A:T	W3501R	1.000
8:112287089:C:A	W3102C	1.000
8:112287089:C:G	W3102C	1.000
8:112289390:C:A	W3041C	1.000
8:112289390:C:G	W3041C	1.000
8:112291535:C:A	W2983C	1.000
8:112291535:C:G	W2983C	1.000
8:112291537:A:G	W2983R	1.000
8:112291537:A:T	W2983R	1.000
8:112292542:C:G	C2928S	1.000
8:112292543:A:T	C2928S	1.000
8:112292562:C:A	W2921C	1.000
8:112292562:C:G	W2921C	1.000
8:112292564:A:G	W2921R	1.000
8:112292564:A:T	W2921R	1.000
8:112292581:C:G	C2915S	1.000
8:112292582:A:T	C2915S	1.000
8:112304752:C:A	W2745C	1.000
8:112304752:C:G	W2745C	1.000
8:112304754:A:G	W2745R	1.000
8:112304754:A:T	W2745R	1.000
8:112304771:C:G	C2739S	1.000
8:112304772:A:G	C2739R	1.000
8:112304772:A:T	C2739S	1.000
8:112306038:C:A	W2680C	1.000
8:112306038:C:G	W2680C	1.000

dbSNP variants (sampled 300 via entrez): RS1000004478 (8:113009604 G>A), RS1000006375 (8:112324678 C>A), RS1000009599 (8:113298810 A>G), RS1000013869 (8:113123660 C>T), RS1000016000 (8:112438094 T>A), RS1000017366 (8:113077746 G>A), RS1000017912 (8:113320306 T>A), RS1000019063 (8:112408853 C>G), RS1000025673 (8:112661760 A>C), RS1000027719 (8:112922017 T>C), RS1000030207 (8:113284098 G>A), RS1000031135 (8:112953265 A>G), RS1000031844 (8:112948682 T>G), RS1000036400 (8:112915800 A>G), RS1000036765 (8:112870932 GT>G)

Disease associations

OMIM: gene MIM:608399 | disease phenotypes: MIM:607174, MIM:600176

GenCC curated gene-disease

Disease	Classification	Inheritance
complex neurodevelopmental disorder	Limited	Autosomal dominant

Mondo (6): primary ovarian failure (MONDO:0005387), familial meningioma (MONDO:0011789), pachygyria-intellectual disability-epilepsy syndrome (MONDO:0010840), hemangioma (MONDO:0006500), hereditary breast ovarian cancer syndrome (MONDO:0003582), complex neurodevelopmental disorder (MONDO:0100038)

Orphanet (4): Familial multiple meningioma (Orphanet:263662), Pachygyria-intellectual disability-epilepsy syndrome (Orphanet:2798), Hereditary breast and/or ovarian cancer syndrome (Orphanet:145), NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0001028	Hemangioma

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST001531_13	Temperament	2.000000e-06
GCST001588_4	Periodontal microbiota	2.000000e-06
GCST002104_22	Bronchopulmonary dysplasia	6.000000e-06
GCST002783_313	Body mass index	2.000000e-06
GCST002826_13	Urate levels (BMI interaction)	7.000000e-07
GCST002941_7	Airway imaging phenotypes	3.000000e-07
GCST003123_20	Severe influenza A (H1N1) infection	6.000000e-11
GCST003154_3	Peripheral artery disease	3.000000e-06
GCST003831_32	Asthma	3.000000e-06
GCST003901_2	Cognitive decline (age-related)	3.000000e-07
GCST005790_14	Rosacea symptom severity	7.000000e-06
GCST006606_1	Response to TNF inhibitor in rheumatoid arthritis (change in swollen 28-joint count)	2.000000e-08
GCST006606_13	Response to TNF inhibitor in rheumatoid arthritis (change in swollen 28-joint count)	8.000000e-06
GCST006959_185	Rheumatoid arthritis	7.000000e-10
GCST006959_188	Rheumatoid arthritis	5.000000e-08
GCST007277_12	Tourette syndrome	6.000000e-07
GCST007324_151	Adventurousness	8.000000e-13
GCST009391_1982	Metabolite levels	2.000000e-06
GCST009391_1983	Metabolite levels	3.000000e-06
GCST012297_8	Schizophrenia, bipolar disorder or major depressive disorder	3.000000e-06
GCST012300_3	Schizophrenia, bipolar disorder or major depressive disorder	9.000000e-07

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004825	temperament and character inventory
EFO:0004340	body mass index
EFO:0004531	urate measurement
EFO:0007627	airway imaging measurement
EFO:1001488	influenza A (H1N1)
EFO:0009180	rosacea severity measurement
EFO:0004653	response to TNF antagonist
EFO:0005413	joint damage measurement
EFO:0008579	risk-taking behaviour
EFO:0005058	tyrosine measurement

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D006391	Hemangioma	C04.557.645.375
D061325	Hereditary Breast and Ovarian Cancer Syndrome	C04.588.180.483; C04.588.322.455.431; C04.700.517; C12.050.351.500.056.630.705.431; C12.050.351.937.418.685.431; C12.100.250.056.630.705.431; C12.900.418.685.431; C16.320.700.517; C17.800.090.500.483; C19.344.410.431; C19.391.630.705.431
D016649	Primary Ovarian Insufficiency	C12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750
C538091	Kuzniecky syndrome (supp.)
C537443	Meningioma, familial (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2432742	CSMD3		0.00	0
rs10505168	CSMD3, MIR2053		0.00	0

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation, increases mutagenesis	3
Aflatoxin B1	increases methylation, decreases expression, decreases methylation	3
Valproic Acid	affects expression, decreases methylation	2
bisphenol A	affects cotreatment, decreases methylation	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaminophen	decreases expression	1
Allergens	increases expression	1
Arsenic	affects methylation	1
Methapyrilene	decreases methylation	1
Cyclosporine	decreases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_9T20	OV-4453	Cancer cell line	Female
CVCL_A1SN	TOV-3121EP	Cancer cell line	Female
CVCL_A7NI	2XSB	Cancer cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00417066	PHASE4	COMPLETED	Flexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693	PHASE4	COMPLETED	Evaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616	PHASE4	COMPLETED	Estrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501	PHASE4	UNKNOWN	Effects of ADSC Therapy in Women With POF
NCT02783937	PHASE4	COMPLETED	Filgrastim for Premature Ovarian Insufficiency
NCT03535480	PHASE4	UNKNOWN	Autologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
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
NCT00140998	PHASE3	COMPLETED	Estrogen Treatment (Oral vs. Patches) in Turner Syndrome
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
NCT00001951	PHASE2	COMPLETED	Hormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019	PHASE2	WITHDRAWN	Effects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494	PHASE2	COMPLETED	GnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852	PHASE2	SUSPENDED	The Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467	PHASE2	UNKNOWN	Prevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982	PHASE2	COMPLETED	The Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
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