CRACR2A

gene
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Also known as MGC4266RAB46

Summary

CRACR2A (calcium release activated channel regulator 2A, HGNC:28657) is a protein-coding gene on chromosome 12p13.32, encoding EF-hand calcium-binding domain-containing protein 4B (Q9BSW2). Ca(2+)-binding protein that plays a key role in store-operated Ca(2+) entry (SOCE) in T-cells by regulating CRAC channel activation.

Enables GTPase activity and calcium ion binding activity. Involved in several processes, including activation of store-operated calcium channel activity; positive regulation of JNK cascade; and store-operated calcium entry. Located in several cellular components, including Golgi apparatus; Weibel-Palade body; and immunological synapse.

Source: NCBI Gene 84766 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): combined immunodeficiency (Limited, ClinGen)
  • GWAS associations: 8
  • Clinical variants (ClinVar): 159 total — 1 pathogenic
  • Phenotypes (HPO): 1
  • Druggable target: yes
  • MANE Select transcript: NM_001144958

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28657
Approved symbolCRACR2A
Namecalcium release activated channel regulator 2A
Location12p13.32
Locus typegene with protein product
StatusApproved
AliasesMGC4266, RAB46
Ensembl geneENSG00000130038
Ensembl biotypeprotein_coding
OMIM614178
Entrez84766

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000252322, ENST00000333750, ENST00000440314, ENST00000514026, ENST00000535292, ENST00000535507, ENST00000893446, ENST00000893447, ENST00000893448, ENST00000944630, ENST00000944631, ENST00000944632, ENST00000944633

RefSeq mRNA: 2 — MANE Select: NM_001144958 NM_001144958, NM_032680

CCDS: CCDS44803, CCDS8522

Canonical transcript exons

ENST00000440314 — 20 exons

ExonStartEnd
ENSE0000136663837329423733210
ENSE0000137186937132373713317
ENSE0000163145636153283615439
ENSE0000164945536542123654399
ENSE0000168328836563113656406
ENSE0000168520736789153679098
ENSE0000171047136734463673592
ENSE0000174497536802383680349
ENSE0000174641136381243638454
ENSE0000175019836595643659654
ENSE0000176479736485423648613
ENSE0000221437737530153753109
ENSE0000226053336967723697035
ENSE0000347283636276253627706
ENSE0000347488036192713619372
ENSE0000349907636274363627550
ENSE0000352969036445953644640
ENSE0000364908036417323641838
ENSE0000367855236169543617030
ENSE0000368101336336043633736

Expression profiles

Bgee: expression breadth ubiquitous, 210 present calls, max score 97.54.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8524 / max 193.3725, expressed in 852 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1289941.9841627
1289950.5029265
1289960.177477
1289970.151553
1289920.036511

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183197.54gold quality
ileal mucosaUBERON:000033196.07gold quality
mucosa of sigmoid colonUBERON:000499394.12gold quality
nasal cavity epitheliumUBERON:000538493.45gold quality
colonic mucosaUBERON:000031791.97gold quality
nasal cavity mucosaUBERON:000182691.54gold quality
saliva-secreting glandUBERON:000104488.45gold quality
rectumUBERON:000105288.44gold quality
olfactory segment of nasal mucosaUBERON:000538688.28gold quality
tracheaUBERON:000312687.00gold quality
minor salivary glandUBERON:000183086.09gold quality
bone marrow cellCL:000209285.85gold quality
bronchial epithelial cellCL:000232885.41gold quality
mucosa of paranasal sinusUBERON:000503085.40gold quality
bronchusUBERON:000218585.08gold quality
pancreatic ductal cellCL:000207984.86silver quality
colonic epitheliumUBERON:000039784.56gold quality
epithelium of nasopharynxUBERON:000195184.34gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.22gold quality
mucosa of transverse colonUBERON:000499183.01gold quality
granulocyteCL:000009482.74gold quality
mouth mucosaUBERON:000372982.69gold quality
thymusUBERON:000237082.48gold quality
palpebral conjunctivaUBERON:000181281.74gold quality
tonsilUBERON:000237281.49gold quality
bloodUBERON:000017881.44gold quality
upper leg skinUBERON:000426281.11gold quality
small intestine Peyer’s patchUBERON:000345480.86gold quality
amniotic fluidUBERON:000017380.52gold quality
small intestineUBERON:000210880.26gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.40
E-MTAB-7606no1080.02
E-GEOD-100618no436.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting CRACR2A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-480399.9871.993117
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-971899.9468.91918
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-545-5P99.6670.182308
HSA-MIR-1287-3P99.6366.93492
HSA-MIR-612699.6268.09996
HSA-MIR-6758-3P99.5767.551078
HSA-MIR-18A-3P99.5665.681092
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-431699.3765.751360
HSA-MIR-807099.0769.301303
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-42198.9067.041883
HSA-MIR-3124-3P98.8768.952123
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-4700-5P98.6367.431915
HSA-MIR-628-5P98.3667.74844
HSA-MIR-808997.7466.211698
HSA-MIR-3144-5P97.6465.45646
HSA-MIR-4667-5P97.6166.671683
HSA-MIR-1910-5P97.4266.36844
HSA-MIR-3616-3P96.9665.45983
HSA-MIR-874-5P96.9363.921014
HSA-MIR-3126-5P96.8765.83912
HSA-MIR-6875-5P96.8765.49958
HSA-MIR-390796.7665.04662

Literature-anchored findings (GeneRIF, showing 7)

  • CRACR2A interacts directly with Orai1 and STIM1, forming a ternary complex that dissociates at elevated Ca(2+) concentrations; is a key regulator of CRAC channel-mediated SOCE (PMID:20418871)
  • endothelial cells contain a long variant of CRACR2A which is an EF-hand-containing Rab protein that lacks impact on CRAC channels (PMID:25475730)
  • GTP binding and prenylation of CRACR2A were associated with its localization near the Golgi and its stability (PMID:27016526)
  • Results show the characterization of CRACR2A protein which encodes a large Rab GTPase containing multiple functional domains contrary to small Rab GTPases. It was found to play an unexpected role in regulating intracellular signaling pathways important for T cell activation. (PMID:27221160)
  • There is a significant association between the EFCAB4B gene and localized periodontitis. (PMID:30284742)
  • Vigorous physical activity before diagnosis is associated with epigenetic alterations of CRACR2A and prostate cancer metastatic-lethal progression. (PMID:30464020)
  • These data demonstrate for the first time that a Rab GTPase, Rab46, integrates G protein and Ca(2+) signals to couple on-demand histamine signals to selective Weibel-Palade bodies (WPBs) trafficking. (PMID:31092558)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocracr2abENSDARG00000045758
danio_rerioCRACR2AENSDARG00000068231
mus_musculusCracr2aENSMUSG00000061414
rattus_norvegicusCracr2aENSRNOG00000053449

Paralogs (1): CRACR2B (ENSG00000177685)

Protein

Protein identifiers

EF-hand calcium-binding domain-containing protein 4BQ9BSW2 (reviewed: Q9BSW2)

Alternative names: Calcium release-activated calcium channel regulator 2A, Calcium release-activated channel regulator 2A, Ras-related protein Rab-46

All UniProt accessions (3): Q9BSW2, H0YFI5, H7BXT2

UniProt curated annotations — full annotation on UniProt →

Function. Ca(2+)-binding protein that plays a key role in store-operated Ca(2+) entry (SOCE) in T-cells by regulating CRAC channel activation. Acts as a cytoplasmic calcium-sensor that facilitates the clustering of ORAI1 and STIM1 at the junctional regions between the plasma membrane and the endoplasmic reticulum upon low Ca(2+) concentration. It thereby regulates CRAC channel activation, including translocation and clustering of ORAI1 and STIM1. Upon increase of cytoplasmic Ca(2+) resulting from opening of CRAC channels, dissociates from ORAI1 and STIM1, thereby destabilizing the ORAI1-STIM1 complex. Rab GTPase that mediates the trafficking of Weibel-Palade bodies (WPBs) to microtubule organizing center (MTOC) in endothelial cells in response to acute inflammatory stimuli. During histamine (but not thrombin) stimulation of endothelial cells, the dynein-bound form induces retrograde transport of a subset of WPBs along microtubules to the MTOC in a Ca(2+)-independent manner and its GTPase activity is essential for this function. Ca(2+)-regulated dynein adapter protein that activates dynein-mediated transport and dynein-dynactin motility on microtubules and regulates endosomal trafficking of CD47. Acts as an intracellular signaling module bridging two important T-cell receptor (TCR) signaling pathways, Ca(2+)-NFAT and JNK, to affect T-cell activation. In resting T-cells, is predominantly localized near TGN network in a GTP-bound form, upon TCR stimulation, localizes at the immunological synapse via interaction with VAV1 to activate downstream Ca(2+)-NFAT and JNK signaling pathways. Plays a role in T-helper 1 (Th1) cell differentiation and T-helper 17 (Th17) cell effector function. Plays a role in store-operated Ca(2+) entry (SOCE) in T-cells by regulating CRAC channel activation.

Subunit / interactions. Interacts with ORAI1 and STIM1; the interaction is direct and takes place in absence of Ca(2+). Forms a complex with ORAI1 and STIM1 at low concentration of Ca(2+), the complex dissociates at elevated Ca(2+) concentrations. Interacts with ORAI2 and ORAI3. Interacts with DYNC1H1. Interacts with the dynein-dynactin complex in a Ca(2+)-dependent manner. Interacts with VAV1.

Subcellular location. Cytoplasm Cytoplasm. Cytoplasm. Cytoskeleton. Microtubule organizing center. Cell membrane. Golgi apparatus membrane. Golgi apparatus. trans-Golgi network membrane. Vesicle.

Tissue specificity. Expressed in the Jurkat T-cell line. Expressed in endothelial cells. Expressed in Weibel-Palade bodies (which are P-selectin/SELP negative) in endothelial cells. Expressed in the Jurkat T-cell line.

Similarity. Belongs to the EFCAB4 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BSW2-22, CRACR2A-L, CRACR2A-Ayes
Q9BSW2-11, CRACR2A-S, CRACR2A-C

RefSeq proteins (2): NP_001138430, NP_116069 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001806Small_GTPaseFamily
IPR002048EF_hand_domDomain
IPR005225Small_GTP-bdDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR027417P-loop_NTPaseHomologous_superfamily
IPR050227RabFamily

Pfam: PF00071, PF13499

Catalyzed reactions (Rhea), 1 shown:

  • GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (58 total): binding site 22, mutagenesis site 9, region of interest 6, sequence variant 6, helix 5, strand 3, splice variant 2, chain 1, domain 1, lipid moiety-binding region 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6PSDX-RAY DIFFRACTION2.66

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BSW2-F170.340.36

Functional residue map

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

Ligand- & substrate-binding residues (22): 99; 101; 103; 108; 554; 556; 557; 558; 559; 559; 560; 571

Post-translational modifications (1): 729

Mutagenesis-validated functional residues (9):

PositionPhenotype
63loss of calcium-binding and interaction with the dynein-dynactin complex; when associated with a-65; a-97 and a-99.
65loss of calcium-binding and interaction with the dynein-dynactin complex; when associated with a-63; a-97 and a-99.
97–99in ef2mut; enhanced stim1 clustering and elevated cytoplasmic ca2+, thereby causing cell death in t-cells. loss of calci
97loss of calcium-binding and interaction with the dynein-dynactin complex; when associated with a-63; a-65 and a-99.
99loss of calcium-binding and interaction with the dynein-dynactin complex; when associated with a-63; a-65 and a-97.
559gdp-binding mutant with reduced gtpase activity and protein stability. reduced ability to activate jnk signaling pathway
604gtp-binding mutant with reduced gtpase activity but increased protein stability. increased ability to activate jnk signa
658gtp/gdp-binding defective mutant with reduced gtpase activity and protein stability. failure to localize to the microtub
729–731failure to localize to the golgi membrane.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation

MSigDB gene sets: 118 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GOBP_POSITIVE_REGULATION_OF_CALCIUM_ION_TRANSPORT, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_POSITIVE_REGULATION_OF_CATION_CHANNEL_ACTIVITY, GOCC_SECRETORY_GRANULE, GOBP_T_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_POSITIVE_REGULATION_OF_TRANSPORTER_ACTIVITY, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, GOZGIT_ESR1_TARGETS_DN, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GOBP_VESICLE_MEDIATED_TRANSPORT, CAGCTG_AP4_Q5, GOBP_POSITIVE_REGULATION_OF_TRANSMEMBRANE_TRANSPORT, GOCC_MICROTUBULE_ORGANIZING_CENTER

GO Biological Process (13): store-operated calcium entry (GO:0002115), adaptive immune response (GO:0002250), intracellular protein localization (GO:0008104), vesicle-mediated transport (GO:0016192), endosomal transport (GO:0016197), activation of store-operated calcium channel activity (GO:0032237), response to histamine (GO:0034776), T-helper 1 cell differentiation (GO:0045063), positive regulation of JNK cascade (GO:0046330), positive regulation of calcium ion transport (GO:0051928), immune system process (GO:0002376), monoatomic ion transport (GO:0006811), calcium ion transport (GO:0006816)

GO Molecular Function (8): GTPase activity (GO:0003924), G protein activity (GO:0003925), calcium ion binding (GO:0005509), GTP binding (GO:0005525), nucleotide binding (GO:0000166), protein binding (GO:0005515), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (14): Golgi membrane (GO:0000139), immunological synapse (GO:0001772), extracellular region (GO:0005576), cytoplasm (GO:0005737), microtubule organizing center (GO:0005815), plasma membrane (GO:0005886), membrane (GO:0016020), vesicle (GO:0031982), trans-Golgi network membrane (GO:0032588), Weibel-Palade body (GO:0033093), specific granule lumen (GO:0035580), Golgi apparatus (GO:0005794), cytoskeleton (GO:0005856), specific granule (GO:0042581)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
calcium ion transport2
transport2
secretory granule2
immune response1
macromolecule localization1
cellular process1
vesicle-mediated transport1
intracellular transport1
positive regulation of store-operated calcium channel activity1
response to nitrogen compound1
alpha-beta T cell activation involved in immune response1
T cell differentiation involved in immune response1
T-helper 1 type immune response1
T-helper cell differentiation1
JNK cascade1
positive regulation of MAPK cascade1
regulation of JNK cascade1
positive regulation of monoatomic ion transport1
regulation of calcium ion transport1
biological_process1
metal ion transport1
ribonucleoside triphosphate phosphatase activity1
GTPase activity1
molecular function regulator activity1
metal ion binding1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
catalytic activity1
cation binding1
Golgi apparatus1
bounding membrane of organelle1
plasma membrane1
intracellular anatomical structure1
microtubule cytoskeleton1
membrane1
cell periphery1

Protein interactions and networks

STRING

818 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CRACR2ASTIM1Q13586922
CRACR2AORAI1Q96D31766
CRACR2ASARAFQ96BY9745
CRACR2ASTIMATEQ86TL2698
CRACR2AEFHBQ8N7U6619
CRACR2AC11orf97A0A1B0GVM6583
CRACR2ASTIM2Q9P246558
CRACR2ACALM1P02593530
CRACR2ABICDL1Q6ZP65490
CRACR2AORAI2Q96SN7482
CRACR2ASLC35G1Q2M3R5480
CRACR2ABICDL2A1A5D9466
CRACR2ARAB11FIP3O75154457
CRACR2AORAI3Q9BRQ5456
CRACR2AASPHQ12797447

IntAct

158 interactions, top by confidence:

ABTypeScore
ORAI1STIM1psi-mi:“MI:0914”(association)0.960
TLE5CRACR2Apsi-mi:“MI:0915”(physical association)0.670
CRACR2ATLE5psi-mi:“MI:0915”(physical association)0.670
CLUAP1CRACR2Apsi-mi:“MI:0915”(physical association)0.590
ORAI1CRACR2Apsi-mi:“MI:0407”(direct interaction)0.590
CRACR2AORAI1psi-mi:“MI:0407”(direct interaction)0.590
ORAI1CRACR2Apsi-mi:“MI:0915”(physical association)0.590
CRACR2AHoxa1psi-mi:“MI:0915”(physical association)0.570
MKRN3CRACR2Apsi-mi:“MI:0915”(physical association)0.560
CRACR2ANOTCH2NLApsi-mi:“MI:0915”(physical association)0.560
CDC23CRACR2Apsi-mi:“MI:0915”(physical association)0.560
CRACR2AMKRN3psi-mi:“MI:0915”(physical association)0.560
NOTCH2NLACRACR2Apsi-mi:“MI:0915”(physical association)0.560
CRACR2ALRIF1psi-mi:“MI:0915”(physical association)0.560
CRACR2ASLAIN1psi-mi:“MI:0915”(physical association)0.560
TRAF1CRACR2Apsi-mi:“MI:0915”(physical association)0.560
SORBS3CRACR2Apsi-mi:“MI:0915”(physical association)0.560
DDIT3CRACR2Apsi-mi:“MI:0915”(physical association)0.560
KRT75CRACR2Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (82): CRACR2A (Two-hybrid), CRACR2A (Two-hybrid), CRACR2A (Two-hybrid), NOTCH2NL (Two-hybrid), CRACR2A (Affinity Capture-MS), EIF1AX (Affinity Capture-MS), MCPH1 (Affinity Capture-MS), CRACR2A (Two-hybrid), CRACR2A (PCA), Hoxa1 (Affinity Capture-Western), CRACR2A (Affinity Capture-MS), CRACR2A (Affinity Capture-MS), MCPH1 (Affinity Capture-MS), PLS1 (Affinity Capture-MS), CRACR2A (Two-hybrid)

ESM2 similar proteins: A0JMQ7, A0JP75, A1A600, A2BGP7, B1A193, B1WBU8, B2RPU2, G9G127, H2MTR9, O88869, Q0VFN8, Q2TAA8, Q32LC2, Q3ULW6, Q3UP38, Q4R7V1, Q4V7B0, Q5EB20, Q5JU67, Q5PQQ9, Q5RDE3, Q5U4W1, Q5XIR4, Q61043, Q6AXZ4, Q6IP02, Q6IQY5, Q6IRU7, Q6NRK1, Q6NRX3, Q6PA69, Q6ZQ12, Q7Z3E5, Q86YF9, Q86YS3, Q8BIJ7, Q8BQP8, Q8CGZ2, Q8CJ96, Q8K342

Diamond homologs: A0JP75, A1A600, B0BNK9, Q3UP38, Q7Z6P3, Q80ZJ8, Q8CB87, Q8N4Y2, Q9BSW2, Q619T5, A4FV54, A5WW21, C4YL11, F1PTE3, O24466, O42819, P07560, P0CY30, P0CY31, P10536, P11620, P16976, P17609, P17610, P20790, P20791, P22125, P22127, P22128, P24409, P28186, P28187, P28188, P31584, P33723, P34139, P34140, P35280, P35286, P36861

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance119
Likely benign9
Benign19

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1047901GRCh37/hg19 12p13.32(chr12:3619010-5221363)Pathogenic

SpliceAI

4741 predictions. Top by Δscore:

VariantEffectΔscore
12:3615439:CCT:Cacceptor_loss1.0000
12:3615440:C:CCacceptor_gain1.0000
12:3615441:T:Gacceptor_loss1.0000
12:3617029:TCC:Tacceptor_loss1.0000
12:3617031:C:CCacceptor_gain1.0000
12:3617031:C:Gacceptor_loss1.0000
12:3617032:T:Cacceptor_loss1.0000
12:3619222:C:Adonor_gain1.0000
12:3619371:TCCTG:Tacceptor_loss1.0000
12:3619373:C:CGacceptor_loss1.0000
12:3619374:T:Aacceptor_loss1.0000
12:3627430:GCTCA:Gdonor_loss1.0000
12:3627431:CTCA:Cdonor_loss1.0000
12:3627432:TCA:Tdonor_loss1.0000
12:3627433:CACCT:Cdonor_loss1.0000
12:3627434:A:Cdonor_loss1.0000
12:3654205:GACTC:Gdonor_loss1.0000
12:3654206:ACTCA:Adonor_loss1.0000
12:3654207:C:CGdonor_loss1.0000
12:3654208:TCACA:Tdonor_loss1.0000
12:3654209:CAC:Cdonor_loss1.0000
12:3654210:A:ACdonor_gain1.0000
12:3654210:A:AGdonor_loss1.0000
12:3654211:C:CAdonor_gain1.0000
12:3654211:CAT:Cdonor_gain1.0000
12:3654211:CATCT:Cdonor_gain1.0000
12:3654212:ATCT:Adonor_gain1.0000
12:3654215:T:TAdonor_gain1.0000
12:3654395:TCCAG:Tacceptor_gain1.0000
12:3654396:CCAG:Cacceptor_gain1.0000

AlphaMissense

4825 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:3617001:G:CS688R0.993
12:3617001:G:TS688R0.993
12:3617003:T:GS688R0.993
12:3680299:A:CF93L0.993
12:3680299:A:TF93L0.993
12:3680301:A:GF93L0.993
12:3627643:T:GD600A0.992
12:3627647:A:GW599R0.991
12:3627647:A:TW599R0.991
12:3627495:A:CY625D0.989
12:3627644:C:GD600H0.989
12:3627643:T:AD600V0.988
12:3680251:G:CF109L0.988
12:3680251:G:TF109L0.988
12:3680253:A:GF109L0.988
12:3633666:T:AK558M0.987
12:3633685:C:GG552R0.987
12:3680252:A:GF109S0.987
12:3633669:C:TG557E0.986
12:3633684:C:AG552V0.986
12:3680267:A:GL104P0.986
12:3619328:C:AK659N0.985
12:3619328:C:GK659N0.985
12:3619331:A:CN658K0.985
12:3619331:A:TN658K0.985
12:3627642:G:CD600E0.985
12:3627642:G:TD600E0.985
12:3633667:T:GK558Q0.985
12:3633669:C:AG557V0.985
12:3627453:A:GW639R0.984

dbSNP variants (sampled 300 via entrez): RS1000029054 (12:3732915 C>A,G,T), RS1000033142 (12:3743243 T>A), RS1000070178 (12:3725178 C>T), RS1000107562 (12:3744429 T>A), RS1000169471 (12:3638956 G>A), RS1000185441 (12:3720042 C>T), RS1000194428 (12:3697811 T>A), RS1000221973 (12:3723475 C>T), RS1000232502 (12:3679707 G>A,T), RS1000271139 (12:3710680 C>A,T), RS1000285487 (12:3636608 A>C), RS1000294996 (12:3645282 G>A,C), RS1000299566 (12:3632690 C>A,G), RS1000393544 (12:3685842 G>A), RS1000422729 (12:3713798 G>A)

Disease associations

OMIM: gene MIM:614178 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
combined immunodeficiencyLimitedAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
combined immunodeficiencyLimitedAR

Mondo (2): microcephaly (MONDO:0001149), combined immunodeficiency (MONDO:0015131)

Orphanet (0):

HPO phenotypes

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

HPOTerm
HP:0000252Microcephaly

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000412_4Male infertility4.000000e-06
GCST000766_9Non-alcoholic fatty liver disease histology (lobular)8.000000e-07
GCST001272_5Cytomegalovirus antibody response5.000000e-06
GCST002248_9Fasting insulin (dietary factor interaction)8.000000e-06
GCST002253_1Homeostasis model assessment of insulin resistance (dietary factor interaction)9.000000e-06
GCST007197_1Chronic periodontitis (localised)2.000000e-08
GCST012490_378Femur bone mineral density x serum urate levels interaction3.000000e-08
GCST90026413_2Severe insulin-deficient type 2 diabetes4.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0008111diet measurement
EFO:0004501HOMA-IR
EFO:0004531urate measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3638353 (SINGLE PROTEIN)

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

Binding affinities (BindingDB)

56 measured of 56 human assays (56 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-3-fluoropyridine-4-carboxamideIC5020.4 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-5-methyl-1,2-oxazole-4-carboxamideIC5020.8 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]-2-methylbenzamideIC5023 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-2,3-difluorobenzamideIC5032.6 nMUS-8921364: Modulators of calcium release-activated calcium channel
4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-N-(4-methyl-1,3-thiazol-5-yl)benzamideIC5034.1 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-4-methylthiadiazole-5-carboxamideIC5035.7 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]-2-methylbenzamideIC5036.4 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]-3-fluoropyridine-4-carboxamideIC5037.6 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]pyridine-3-carboxamideIC5047.2 nMUS-8921364: Modulators of calcium release-activated calcium channel
4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-N-[(4-methyl-1,3-thiazol-5-yl)methyl]anilineIC5048 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-4-methyl-1,3-thiazole-5-carboxamideIC5048.2 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-2-pyridin-3-ylacetamideIC5048.2 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]-2,6-difluorobenzamideIC5050.6 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-(difluoromethyl)-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-4-methyl-1,3-thiazole-5-carboxamideIC5052.6 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]-2-fluorobenzamideIC5060 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)-3-fluorophenyl]-4-methylthiadiazole-5-carboxamideIC5060.3 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]-4-methylthiadiazole-5-carboxamideIC5062.4 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]pyridine-4-carboxamideIC5062.6 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-5-methyl-1,2-oxazole-4-carboxamideIC5063.2 nMUS-8921364: Modulators of calcium release-activated calcium channel
3,5-dichloro-N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]pyridine-4-carboxamideIC5065.5 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]-2,3-difluorobenzamideIC5070.3 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-4-methyl-1,3-thiazole-5-carboxamideIC5072 nMUS-8921364: Modulators of calcium release-activated calcium channel
6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-N-(2,6-difluorophenyl)pyridine-3-carboxamideIC5072.1 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-4-methylpyrimidine-5-carboxamideIC5081.2 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-2,6-difluorobenzamideIC5098.6 nMUS-8921364: Modulators of calcium release-activated calcium channel
4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-N-(2,6-difluorophenyl)-3-fluorobenzamideIC5099.7 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-2-methylbenzamideIC50120 nMUS-8921364: Modulators of calcium release-activated calcium channel
4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-N-(2,6-difluorophenyl)benzamideIC50124 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-3,5-dimethyl-1,2-oxazole-4-carboxamideIC50124 nMUS-8921364: Modulators of calcium release-activated calcium channel
3,5-dichloro-N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]pyridine-4-carboxamideIC50130 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]pyridine-4-carboxamideIC50141 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)-3-fluorophenyl]-2,6-difluorobenzamideIC50145 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-2-methylbenzamideIC50147 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[6-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-pyridinyl]-4-methylthiadiazole-5-carboxamideIC50150 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]-3-fluoropyridine-4-carboxamideIC50159 nMUS-8921364: Modulators of calcium release-activated calcium channel
3,5-dichloro-N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]pyridine-4-carboxamideIC50159 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(4-chloro-3,5-dicyclopropylpyrazol-1-yl)-3-fluorophenyl]-4-methylthiadiazole-5-carboxamideIC50181 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-4-methylthiadiazole-5-carboxamideIC50184 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)-3-fluorophenyl]pyridine-4-carboxamideIC50185 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[4-chloro-5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-4-methyl-1,3-thiazole-5-carboxamideIC50194 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]pyridine-3-carboxamideIC50206 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]-4-methyl-1,3-thiazole-5-carboxamideIC50207 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)-3-fluorophenyl]-4-methylpyrimidine-5-carboxamideIC50224 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]-3-fluorophenyl]pyridine-4-carboxamideIC50232 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]-3-fluoropyridine-4-carboxamideIC50244 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]pyridine-4-carboxamideIC50255 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-(3,5-dicyclopropylpyrazol-1-yl)phenyl]-5-methyl-1,2-oxazole-4-carboxamideIC50256 nMUS-8921364: Modulators of calcium release-activated calcium channel
1-[4-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-3-(4-methyl-1,3-thiazol-5-yl)ureaIC50269 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[2-[5-cyclopropyl-3-(trifluoromethyl)pyrazol-1-yl]pyrimidin-5-yl]-2,6-difluorobenzamideIC50295 nMUS-8921364: Modulators of calcium release-activated calcium channel
N-[4-[5-(fluoromethyl)-3-(trifluoromethyl)pyrazol-1-yl]phenyl]-4-methyl-1,3-thiazole-5-carboxamideIC50373 nMUS-8921364: Modulators of calcium release-activated calcium channel

ChEMBL bioactivities

56 potent at pChembl≥5 of 56 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.69IC5020.37nMCHEMBL3666849
7.68IC5020.79nMCHEMBL3666859
7.64IC5022.96nMCHEMBL3666871
7.49IC5032.59nMCHEMBL3666861
7.47IC5034.11nMCHEMBL3666854
7.45IC5035.72nMCHEMBL3666857
7.44IC5036.35nMCHEMBL3666830
7.42IC5037.58nMCHEMBL3666877
7.33IC5047.21nMCHEMBL3666875
7.32IC5048.22nMCHEMBL3666851
7.32IC5048.02nMCHEMBL3666852
7.32IC5048.17nMCHEMBL3666858
7.30IC5050.58nMCHEMBL3666874
7.28IC5052.62nMCHEMBL3666881
7.22IC5060.31nMCHEMBL3639657
7.22IC5060nMCHEMBL3666872
7.21IC5062.44nMCHEMBL3666827
7.20IC5063.17nMCHEMBL3666845
7.20IC5062.56nMCHEMBL3666876
7.18IC5065.49nMCHEMBL3666842
7.15IC5070.32nMCHEMBL3666873
7.14IC5072.03nMCHEMBL3666844
7.14IC5072.11nMCHEMBL3666878
7.09IC5081.25nMCHEMBL3666867
7.01IC5098.58nMCHEMBL3666862
7.00IC5099.71nMCHEMBL3666869
6.92IC50119.7nMCHEMBL3666847
6.91IC50124.5nMCHEMBL3666846
6.91IC50123.8nMCHEMBL3666855
6.89IC50129.6nMCHEMBL3666833
6.85IC50141.3nMCHEMBL3666831
6.84IC50145.1nMCHEMBL3666836
6.83IC50147.2nMCHEMBL3666860
6.83IC50149.6nMCHEMBL3666870
6.80IC50159.1nMCHEMBL3666865
6.80IC50159.3nMCHEMBL3666866
6.74IC50181.1nMCHEMBL3666839
6.74IC50183.6nMCHEMBL3666843
6.73IC50184.6nMCHEMBL3666837
6.71IC50194nMCHEMBL3666856
6.69IC50205.7nMCHEMBL3666863
6.68IC50206.7nMCHEMBL3666828
6.65IC50223.5nMCHEMBL3666838
6.63IC50232nMCHEMBL3666864
6.61IC50243.9nMCHEMBL3666832
6.59IC50256.1nMCHEMBL3666829
6.59IC50254.7nMCHEMBL3666848
6.57IC50269nMCHEMBL3666853
6.53IC50295.4nMCHEMBL3666879
6.43IC50373.4nMCHEMBL3666880

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1increases methylation2
aristolochic acid Idecreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamideincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
beta-lapachoneincreases expression1
butyraldehydeincreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)increases expression1
aflatoxin B2increases methylation1
pentanalincreases expression1
di-n-butylphosphoric acidaffects expression1
entinostatincreases expression1
abrinedecreases expression1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinoneincreases expression1
Arsenic Trioxideincreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Methapyrileneincreases methylation1
Methyl Methanesulfonatedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases expression1
Valproic Acidincreases methylation1
Vanadatesdecreases expression1
Antirheumatic Agentsdecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3705678BindingIn-Vitro Inhibition Assay: Inhibition of CRAC channels was determined following thapsigargin (Sigma, Cat # T9033) induced endoplasmic calcium release in Jurkat cells. (see Yasurio Yonetoky et. al Bio. & Med. Chem. 14 (2006) 4750-4760). CellModulators of calcium release-activated calcium channel

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02737384PHASE2TERMINATEDHematopoietic Stem Cells Transplantation in Children With Combined Immunodeficiency (CID)
NCT02915406Not specifiedNO_LONGER_AVAILABLEcliniMACs HUD for T Cell Depletion
NCT04902807Not specifiedRECRUITINGConception of a Diagnosis, Prognosis and Therapeutic Decision Tool for Patients With Autoimmunity and Inflammation
NCT06659588Not specifiedRECRUITINGStudy of Populations at Risk of Developing Chronic Hepatitis Linked to Chronic Enteric Virus Infection in Patients With Primary Immunodeficiency and Secondary Humoral Deficiency
NCT05518188PHASE1/PHASE2RECRUITINGMelpida: Recombinant Adeno-associated Virus (serotype 9) Encoding a Codon Optimized Human AP4M1 Transgene (hAP4M1opt)
NCT00001639Not specifiedCOMPLETEDEvaluation of Patients With Unresolved Chromosome Abnormalities
NCT01151462Not specifiedWITHDRAWNPostnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
NCT01565005Not specifiedCOMPLETEDMicrocephaly Genetic Deficiency in Neural Progenitors
NCT02510170Not specifiedCOMPLETEDFetal and Maternal Head Circumference During Pregnancy in Israeli Population
NCT02741882Not specifiedCOMPLETEDZika and Microcephaly: Case-control Study
NCT02943304Not specifiedCOMPLETEDNeurodevelopment Outcome of Newborns Exposed to Zika Virus (ZIKV) in Utero
NCT03255369Not specifiedUNKNOWNVertical Exposure to Zika Virus and Its Consequences for Child Neurodevelopment (ZIKVIRUSIFF)
NCT03325946Not specifiedRECRUITINGThe FBRI VTC Neuromotor Research Clinic
NCT03330600Not specifiedCOMPLETEDEfficacy of Aquatic Physiotherapy in Children With Microcephaly by Zika Virus Congenital Syndrome
NCT03548779Not specifiedCOMPLETEDNorth Carolina Genomic Evaluation by Next-generation Exome Sequencing, 2
NCT03651687Not specifiedCOMPLETEDGuangzhou Surveillance and Clinical Study in Microcephaly (GSCSM)
NCT03922594Not specifiedTERMINATEDSurveillance of Zika-related Microcephaly in Sub-Saharan Africa and Asia
NCT04816175Not specifiedCOMPLETEDIntensive Therapy for Children With Microcephaly, Hyperkinetic Movements, or Global Developmental Delay
NCT05322980Not specifiedCOMPLETEDSummary of Infants Weighing 500 Grams or Less
NCT06019182Not specifiedRECRUITINGMEHMO Natural History and Biomarkers
NCT06566066Not specifiedRECRUITINGRegister for Patients With Thyroid Hormone Resistance.