IL7R

gene
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Also known as CD127IL7RAlnc-IL7RIL-7RalphaIL7RalphasIL-7RCDw127

Summary

IL7R (interleukin 7 receptor, HGNC:6024) is a protein-coding gene on chromosome 5p13.2, encoding Interleukin-7 receptor subunit alpha (P16871). Receptor for interleukin-7.

The protein encoded by this gene is a receptor for interleukin 7 (IL7). The function of this receptor requires the interleukin 2 receptor, gamma chain (IL2RG), which is a common gamma chain shared by the receptors of various cytokines, including interleukins 2, 4, 7, 9, and 15. This protein has been shown to play a critical role in V(D)J recombination during lymphocyte development. Defects in this gene may be associated with severe combined immunodeficiency (SCID). Alternatively spliced transcript variants have been found.

Source: NCBI Gene 3575 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): immunodeficiency 104 (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 43
  • Clinical variants (ClinVar): 605 total — 46 pathogenic, 15 likely-pathogenic
  • Phenotypes (HPO): 59
  • Cancer driver (intOGen): activating (oncogene-like) across 4 cancer types
  • MANE Select transcript: NM_002185

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6024
Approved symbolIL7R
Nameinterleukin 7 receptor
Location5p13.2
Locus typegene with protein product
StatusApproved
AliasesCD127, IL7RA, lnc-IL7R, IL-7Ralpha, IL7Ralpha, sIL-7R, CDw127
Ensembl geneENSG00000168685
Ensembl biotypeprotein_coding
OMIM146661
Entrez3575

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 7 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000303115, ENST00000505093, ENST00000505875, ENST00000506850, ENST00000508941, ENST00000509668, ENST00000511031, ENST00000511982, ENST00000514217, ENST00000515665, ENST00000877114

RefSeq mRNA: 2 — MANE Select: NM_002185 NM_001410734, NM_002185

CCDS: CCDS3911

Canonical transcript exons

ENST00000303115 — 8 exons

ExonStartEnd
ENSE000011302693587348035873648
ENSE000011302743587105635871213
ENSE000011302823586730635867463
ENSE000018050073587598335879603
ENSE000020476863585689135857059
ENSE000034754483587551235875587
ENSE000036667593587444935874542
ENSE000036671353586085235860990

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 97.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 51.0899 / max 3672.3247, expressed in 1029 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
5611027.3324686
5611119.0782898
561121.9516204
561090.7694234
561080.6947230
561040.6290151
561130.513757
561050.121059

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lungUBERON:000216797.85gold quality
granulocyteCL:000009497.14gold quality
lymph nodeUBERON:000002996.99gold quality
lower lobe of lungUBERON:000894996.62gold quality
epithelium of nasopharynxUBERON:000195196.15gold quality
nasopharynxUBERON:000172896.13gold quality
vermiform appendixUBERON:000115495.94gold quality
bloodUBERON:000017895.38gold quality
thymusUBERON:000237095.07gold quality
upper lobe of left lungUBERON:000895294.78gold quality
upper lobe of lungUBERON:000894894.73gold quality
gall bladderUBERON:000211094.10gold quality
lungUBERON:000204893.39gold quality
caecumUBERON:000115392.89gold quality
spleenUBERON:000210692.74gold quality
visceral pleuraUBERON:000240192.74gold quality
colonic epitheliumUBERON:000039792.18gold quality
small intestine Peyer’s patchUBERON:000345491.93gold quality
amniotic fluidUBERON:000017391.05gold quality
small intestineUBERON:000210890.20gold quality
jejunal mucosaUBERON:000039990.08gold quality
bone marrowUBERON:000237189.41gold quality
tonsilUBERON:000237288.92gold quality
rectumUBERON:000105288.85gold quality
trabecular bone tissueUBERON:000248388.16gold quality
superficial temporal arteryUBERON:000161487.91gold quality
bone marrow cellCL:000209287.57gold quality
ileal mucosaUBERON:000033187.32gold quality
pleuraUBERON:000097787.23gold quality
parietal pleuraUBERON:000240086.59gold quality

Single-cell (SCXA)

Detected in 48 experiment(s), a significant marker in 37.

ExperimentMarker?Max mean expression
E-CURD-46yes3376.74
E-MTAB-8142yes3013.77
E-CURD-120yes2795.48
E-MTAB-10553yes2745.88
E-CURD-112yes2710.99
E-CURD-88yes2530.67
E-CURD-122yes2472.53
E-GEOD-150728yes2351.19
E-HCAD-36yes2323.57
E-MTAB-6678yes2064.91
E-MTAB-10042yes1976.12
E-MTAB-9221yes1957.26
E-HCAD-1yes1893.19
E-MTAB-10855yes1829.62
E-HCAD-15yes1803.04

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AP1, BRD2, BRD4, ETS1, FOS, FOXO1, FOXP1, GABPA, GATA3, GFI1, IKZF1, JUN, MAFB, MYC, NOTCH1, NR3C1, RELA, RUNX1, SPI1, STAT5A, TCF3, ZBTB17

Literature-anchored findings (GeneRIF, showing 40)

  • IL-7 may function to regulate the milieu of the microenvironment by modulating IL-6 secretion by the IL-7R-expressing stromal elements (PMID:12149213)
  • IL-2 signaling can diminish IL-7Ralpha expression via a phosphatidylinositol 3-kinase/Akt-dependent mechanism. (PMID:12354940)
  • IL-7R has a role in some human solid malignancies [review] (PMID:12792903)
  • Interaction between IL-7 and its receptor has the major role in modulating T-ALL survival within the microenvironment generated by the T-ALL/TEC interaction. (PMID:14607751)
  • Expansion of CD8 positive, CD127 negative effector-like T cells is identified as a novel feature of HIV-associated immune perturbation. (PMID:15728501)
  • Maturation of memory CD4 and CD8 T cells is associated with a CD127high phenotype and the expression of CD127 serves as a predictor of the functional quality of antiviral T cells. (PMID:15879083)
  • Virus-specific IL-7Ralpha+ cells proliferated vigorously in response to IL-7, IL-15, or peptide, whereas IL-7Ralpha- cells required both peptide and helper-cell activation or IL-2 or IL-15 for optimal expansion (PMID:15947093)
  • Altogether, we show that gamma(c) is the target of an ubiquitination mechanism and its expression level can be regulated through the activities of a couple of ubiquitin-ligase/ubiquitin-hydrolase enzymes, namely c-Cbl/DUB-2. (PMID:16004964)
  • The T cell proliferation gene IL7R (CD127) was also underexpressed in PPMS, but was up-regulated in SPMS compared to the controls. (PMID:16075257)
  • Aging affects IL-7Ralpha expression by T cells, leading to impaired signaling and survival responses to IL-7. (PMID:16357322)
  • HIV infection produces the Tat protein, which in turn may up-regulate IL-7R in a paracrine manner, which ultimately promotes early events in HIV replication. (PMID:16614257)
  • Transcription of the IL-7R alpha subunit is suppressed in both naive and memory T cells following IL-7 stimulation. (PMID:16709829)
  • Cell surface expression of CD127 therefore allows accurate estimation of regulatory T cell numbers and isolation of pure populations for in vitro studies and should contribute to our understanding of regulatory abnormalities in immunopathic diseases. (PMID:16818676)
  • CD127 can be used to quantitate regulatory T (Treg) cell subsets in individuals with type 1 diabetes supporting the use of CD127 as a biomarker for human Treg cells. (PMID:16818678)
  • CD127 expression on T cells remains low in HIV-infected patients despite antiretroviral therapy (PMID:16837861)
  • IL-7 receptor and Notch1 pathways cooperate to synchronize cell proliferation and suppression of non-T lineage choices in primitive intrathymic progenitors. (PMID:16951331)
  • CD127 uniquely enables the purification of FOXP3+ Treg cells and, potentially, also “adaptive” regulatory T-cell subsets from the CD4+CD25- T-cell population. (PMID:17045841)
  • A large fraction of peripheral HCV-specific CD8+ T cells were CD127+ and KLRG1-. Intrahepatic virus-specific CD8+ T cells displayed significantly reduced levels of CD127 expression but similar levels of KLRG1 expression compared to the peripheral blood. (PMID:17079288)
  • CD4+ regulatory T-cells exhibiting suppressive activity in vitro display distinctly lower surface expression of CD127, irrespective of their level of CD25 expression. (PMID:17173927)
  • results confirm that signal transduction via the IL-15R, and hence NK ontogeny, is preferentially retained relative to the IL-7R as gammac expression becomes limiting. (PMID:17363735)
  • These findings suggest that DNA methylation is involved in regulating IL-7Ralpha expression in T cells via affecting IL-7Ralpha gene promoter activity. (PMID:17442928)
  • gene encoding the IL-7Ralpha chain is polymorphic, and investigation of inhalation allergic patients compared with controls showed significant association with two alleles at position +1237 and +2087 (PMID:17504502)
  • A subset of naive CD8-positive cells characterized by low interleukin-7 receptor alpha message and protein expression may encompass cells that have recently received homeostatic signals. (PMID:17579041)
  • CD4(+)CD25(+)CD45RO(+)IL-7Ralpha(high) cell population contained allospecific CD4 T cells and secreted effector cytokines. (PMID:17591854)
  • Increased constitutive interleukin-7 receptor alpha expression has minimal effects on the numbers or function of effector and memory CD8 T cells formed. (PMID:17609371)
  • Alleles of IL2RA and IL7RA and those in the HLA locus are identified as heritable risk factors for multiple sclerosis. (PMID:17660530)
  • Results provide compelling evidence that polymorphisms in IL7R, which encodes the interleukin 7 receptor alpha chain (IL7Ralpha), indeed contribute to the non-HLA genetic risk in multiple sclerosis. (PMID:17660816)
  • Results show allelic association of a polymorphism in interleukin 7 receptor alpha chain (IL7R) as a significant risk factor for multiple sclerosis in four independent family-based or case-control data sets. (PMID:17660817)
  • Immunolocalization of IL-7, IL-7Ralpha, SDF-1alpha, and CXCR4 resulted in a diffuse but specific labeling. RT-PCR analysis confirmed the expression of the above-mentioned transcripts. (PMID:17894415)
  • Stimulation of the IL-7 pathway begins with IL-7 binding to unglycosylated and glycosylated forms of its alpha-receptor, IL-7 receptor alpha. (PMID:17909291)
  • Haplotypes of the IL7R gene are correlated with altered expression in whole blood cells in multiple sclerosis. (PMID:17928869)
  • IL-7 reduced CD127-surface expression and shedding by CD8+ T cells; results support a role for IL-7 in the down-regulation of CD127 expression and impairment of CTL function observed in HIV infection (PMID:17956896)
  • We report that loss of CD127 defines terminally differentiated B cell-helping effector T cells in human tonsils. (PMID:18025189)
  • The association between rs6897932 and multiple sclerosis in the Olmsted County collection appeared to be much stronger than anticipated on the basis of recent studies (PMID:18272905)
  • Expression of transgenic IL-7 receptor alpha by itself does not support increased survival of effector antigen-specific CD4 or CD8 T cells into the memory phase following infection with Listeria monocytogenes. (PMID:18292507)
  • IL2RA and IL7RA genes confer susceptibility for multiple sclerosis in two independent European populations. (PMID:18354419)
  • IL-7- and TCR/CD28-mediated signaling data show that differentially regulate IL-7Ralpha expression on human T cells with a transient and chronic effect, respectively. (PMID:18390701)
  • during HIV infection, specific changes in the fraction of CD4(+) T cells expressing CD25 and/or CD127 are associated with disease progression (PMID:18390743)
  • Independent replication of the association between the CAPSL and IL7R locus and type 1 diabetes, especially for early-onset type 1 diabetes patients. (PMID:18563381)
  • Association studies between IL7RA rs6897932 and multiple sclerosis. (PMID:18721276)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusIl7rENSMUSG00000003882
rattus_norvegicusIl7rENSRNOG00000065741

Paralogs (7): IL4R (ENSG00000077238), CSF2RB (ENSG00000100368), IL2RB (ENSG00000100385), IL21R (ENSG00000103522), MPL (ENSG00000117400), IL9R (ENSG00000124334), EPOR (ENSG00000187266)

Protein

Protein identifiers

Interleukin-7 receptor subunit alphaP16871 (reviewed: P16871)

Alternative names: CDw127

All UniProt accessions (6): B8YG18, P16871, D6RCR9, D6RDM4, D6RG28, H0YA41

UniProt curated annotations — full annotation on UniProt →

Function. Receptor for interleukin-7. Also acts as a receptor for thymic stromal lymphopoietin (TSLP).

Subunit / interactions. The IL7 receptor is a heterodimer of IL7R and IL2RG. The TSLP receptor is a heterodimer of CRLF2 and IL7R. Interacts with CD53.

Subcellular location. Cell membrane Cell membrane Secreted.

Post-translational modifications. N-glycosylated IL-7Ralpha binds IL7 300-fold more tightly than the unglycosylated form. Ubiquitinated by MARCHF8; leading to lysosomal degradation.

Disease relevance. Immunodeficiency 104, severe combined (IMD104) [MIM:608971] A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. The disease is caused by variants affecting the gene represented in this entry. Multiple sclerosis 3 (MS3) [MIM:612595] A multifactorial, inflammatory, demyelinating disease of the central nervous system. Sclerotic lesions are characterized by perivascular infiltration of monocytes and lymphocytes and appear as indurated areas in pathologic specimens (sclerosis in plaques). The pathological mechanism is regarded as an autoimmune attack of the myelin sheath, mediated by both cellular and humoral immunity. Clinical manifestations include visual loss, extra-ocular movement disorders, paresthesias, loss of sensation, weakness, dysarthria, spasticity, ataxia and bladder dysfunction. Genetic and environmental factors influence susceptibility to the disease. Disease susceptibility is associated with variants affecting the gene represented in this entry. A polymorphism at position 244 strongly influences susceptibility to multiple sclerosis. Overtransmission of the major ‘C’ allele coding for Thr-244 is detected in offspring affected with multiple sclerosis. In vitro analysis of transcripts from minigenes containing either ‘C’ allele (Thr-244) or ‘T’ allele (Ile-244) shows that the ‘C’ allele results in an approximately two-fold increase in the skipping of exon 6, leading to increased production of a soluble form of IL7R. Thus, the multiple sclerosis associated ‘C’ risk allele of IL7R would probably decrease membrane-bound expression of IL7R. As this risk allele is common in the general population, some additional triggers are probably required for the development and progression of MS.

Domain organisation. The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell-surface receptor binding. The box 1 motif is required for JAK interaction and/or activation.

Similarity. Belongs to the type I cytokine receptor family. Type 4 subfamily.

Isoforms (4)

UniProt IDNamesCanonical?
P16871-11, H20yes
P16871-23, H1
P16871-34, H6, Secreted
P16871-42, Secreted

RefSeq proteins (2): NP_001397663, NP_002176* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003531Hempt_rcpt_S_F1_CSConserved_site
IPR003961FN3_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR040997FN3_7Domain

Pfam: PF00041, PF18447

UniProt features (55 total): strand 17, sequence variant 7, glycosylation site 6, splice variant 4, sequence conflict 4, helix 4, disulfide bond 3, topological domain 2, short sequence motif 2, signal peptide 1, chain 1, transmembrane region 1, turn 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
7OPBX-RAY DIFFRACTION2.14
3UP1X-RAY DIFFRACTION2.15
5J11X-RAY DIFFRACTION2.56
3DI2X-RAY DIFFRACTION2.7
3DI3X-RAY DIFFRACTION2.9
6P50X-RAY DIFFRACTION2.9
6P67X-RAY DIFFRACTION2.9
9XEASOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P16871-F168.520.42

Antibody-complex structures (SAbDab): 26P50, 6P67

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): 282

Disulfide bonds (3): 42–57, 74–82, 108–118

Glycosylation sites (6): 65, 151, 182, 232, 233, 49

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-1266695Interleukin-7 signaling
R-HSA-8856825Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828Clathrin-mediated endocytosis

MSigDB gene sets: 775 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_DNA_RECOMBINATION, GOBP_NEGATIVE_REGULATION_OF_PEPTIDYL_TYROSINE_PHOSPHORYLATION, WALLACE_PROSTATE_CANCER_RACE_UP, GOBP_NEGATIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, MCLACHLAN_DENTAL_CARIES_UP, GOBP_POSITIVE_REGULATION_OF_HEMOPOIESIS, HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, MODULE_169, GOBP_REGULATION_OF_PHOSPHORYLATION, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_RESPONSE_TO_PEPTIDE, GOBP_REGULATION_OF_LEUKOCYTE_APOPTOTIC_PROCESS, GOBP_B_CELL_ACTIVATION

GO Biological Process (26): regulation of DNA recombination (GO:0000018), cell morphogenesis (GO:0000902), B cell homeostasis (GO:0001782), T cell mediated cytotoxicity (GO:0001913), negative regulation of T cell mediated cytotoxicity (GO:0001915), immune response (GO:0006955), signal transduction (GO:0007165), cell surface receptor signaling pathway (GO:0007166), positive regulation of cell population proliferation (GO:0008284), regulation of cell size (GO:0008361), gene expression (GO:0010467), positive regulation of gene expression (GO:0010628), cellular homeostasis (GO:0019725), hemopoiesis (GO:0030097), T cell differentiation in thymus (GO:0033077), positive regulation of T cell differentiation in thymus (GO:0033089), interleukin-7-mediated signaling pathway (GO:0038111), B cell proliferation (GO:0042100), T cell homeostasis (GO:0043029), positive regulation of receptor signaling pathway via JAK-STAT (GO:0046427), lymph node development (GO:0048535), defense response to Gram-positive bacterium (GO:0050830), negative regulation of T cell apoptotic process (GO:0070233), positive regulation of receptor signaling pathway via STAT (GO:1904894), cytokine-mediated signaling pathway (GO:0019221), T cell differentiation (GO:0030217)

GO Molecular Function (4): antigen binding (GO:0003823), cytokine receptor activity (GO:0004896), interleukin-7 receptor activity (GO:0004917), protein binding (GO:0005515)

GO Cellular Component (7): extracellular region (GO:0005576), nucleoplasm (GO:0005654), cytosol (GO:0005829), plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), clathrin-coated endocytic vesicle membrane (GO:0030669), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Signaling by Interleukins1
Clathrin-mediated endocytosis1
Membrane Trafficking1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
lymphocyte homeostasis2
cytokine-mediated signaling pathway2
binding2
DNA recombination1
regulation of DNA metabolic process1
anatomical structure morphogenesis1
leukocyte mediated cytotoxicity1
T cell mediated immunity1
negative regulation of leukocyte mediated cytotoxicity1
T cell mediated cytotoxicity1
regulation of T cell mediated cytotoxicity1
negative regulation of T cell mediated immunity1
immune system process1
response to stimulus1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
signal transduction1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
regulation of cellular component size1
macromolecule biosynthetic process1
gene expression1
regulation of gene expression1
positive regulation of macromolecule biosynthetic process1
homeostatic process1
cell development1
T cell differentiation1
T cell differentiation in thymus1
regulation of T cell differentiation in thymus1
positive regulation of T cell differentiation1
cellular response to interleukin-71
B cell activation1
lymphocyte proliferation1
cell surface receptor signaling pathway via JAK-STAT1
regulation of receptor signaling pathway via JAK-STAT1

Protein interactions and networks

STRING

3203 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
IL7RIL7P13232999
IL7RIL2RGP31785998
IL7RTSLPQ969D9997
IL7RCRLF2Q9HC73997
IL7RIL2P01585942
IL7RJAK1P23458942
IL7RIL15P40933937
IL7RCD8AP01732935
IL7RCD4P01730925
IL7RJAK3P52333919
IL7RIL2RAP01589906
IL7RSTAT5BP51692885
IL7RSTAT5AP42229877
IL7RFOXP3Q9BZS1871
IL7RIL4P05112870

IntAct

75 interactions, top by confidence:

ABTypeScore
IL7IL7Rpsi-mi:“MI:0407”(direct interaction)0.740
IL7IL7Rpsi-mi:“MI:0915”(physical association)0.740
IL7RIL7psi-mi:“MI:0915”(physical association)0.740
CAMKVAP3B1psi-mi:“MI:0914”(association)0.640
VAMP5IL7Rpsi-mi:“MI:0915”(physical association)0.560
TMEM60IL7Rpsi-mi:“MI:0915”(physical association)0.560
CD302IL7Rpsi-mi:“MI:0915”(physical association)0.560
FAM3CIL7Rpsi-mi:“MI:0915”(physical association)0.560
ATP6V0CIL7Rpsi-mi:“MI:0915”(physical association)0.560
IL7RTMEM60psi-mi:“MI:0915”(physical association)0.560
IL7RCD302psi-mi:“MI:0915”(physical association)0.560
IL7RFAM3Cpsi-mi:“MI:0915”(physical association)0.560
IL7RATP6V0Cpsi-mi:“MI:0915”(physical association)0.560
TMEM120BIL7Rpsi-mi:“MI:0915”(physical association)0.560
IL7RMALLpsi-mi:“MI:0915”(physical association)0.560
IL7RAGTRAPpsi-mi:“MI:0915”(physical association)0.560
MS4A1IL7Rpsi-mi:“MI:0915”(physical association)0.560

BioGRID (134): CISH (Affinity Capture-Western), IL7R (Affinity Capture-Western), CISH (Affinity Capture-Western), SOCS1 (Affinity Capture-Western), SOCS2 (Affinity Capture-Western), PIK3R1 (Affinity Capture-Western), IL7R (Two-hybrid), IL7R (Two-hybrid), IL7R (Two-hybrid), IL7R (Two-hybrid), AGTRAP (Two-hybrid), TMEM120B (Two-hybrid), IL7R (Affinity Capture-Western), IL7R (Proximity Label-MS), FYN (Affinity Capture-Western)

ESM2 similar proteins: A0MSX9, A5HJM1, C8AW46, C8AW47, K9JA28, O02671, O35664, O46561, O70458, P05710, P14787, P15260, P15261, P16297, P16471, P16871, P16872, P16882, P26896, P48356, P48357, P48551, P97378, Q08501, Q13651, Q28172, Q28235, Q38IC7, Q38J85, Q3SYS8, Q4W815, Q5VWK5, Q61727, Q62959, Q63257, Q65Z14, Q6JTA8, Q6PHB0, Q80VH0, Q80XZ4

Diamond homologs: A0MSX9, A5HJM1, P16871, P16872, Q38IC7

SIGNOR signaling

5 interactions.

AEffectBMechanism
IL7up-regulatesIL7Rbinding
IL7Rup-regulatesJAK1binding
NOTCH1“up-regulates quantity by expression”IL7R“transcriptional regulation”
NOTCH“up-regulates quantity by expression”IL7R“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 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:

PathwayPartnersFoldFDR
Diseases of signal transduction by growth factor receptors and second messengers514.9×5e-03

GO biological processes:

GO termPartnersFoldFDR
negative regulation of apoptotic process68.0×5e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 4 cancer types — ALL, ESCA, HCC, STAD.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic46
Likely pathogenic15
Uncertain significance212
Likely benign231
Benign66

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1073963NC_000005.9:g.(?35857060)(35857181_?)delPathogenic
1298987NM_002185.5(IL7R):c.616C>T (p.Arg206Ter)Pathogenic
1339483NM_002185.5(IL7R):c.379G>A (p.Val127Ile)Pathogenic
134528NM_002185.5(IL7R):c.662G>T (p.Ser221Ile)Pathogenic
1437489NM_002185.5(IL7R):c.514del (p.Glu172fs)Pathogenic
1453790NM_002185.5(IL7R):c.37del (p.Ser13fs)Pathogenic
1465004NM_002185.5(IL7R):c.126C>G (p.Cys42Trp)Pathogenic
14841NM_002185.5(IL7R):c.538-1G>APathogenic
14842NM_002185.5(IL7R):c.651G>A (p.Trp217Ter)Pathogenic
1706622NM_002185.5(IL7R):c.470del (p.Lys157fs)Pathogenic
208851NM_002185.5(IL7R):c.333T>A (p.Val111=)Pathogenic
2203628NM_002185.5(IL7R):c.562del (p.Lys187_Leu188insTer)Pathogenic
224841NM_002185.5(IL7R):c.361dup (p.Ile121fs)Pathogenic
224842Single allelePathogenic
265195NM_002185.5(IL7R):c.221+2T>GPathogenic
2697973NM_002185.5(IL7R):c.639_640insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCCCTGATCACTATTTT (p.Lys214delinsPhePhePhePhePhePheXaaXaaXaaXaaTer)Pathogenic
2708090NM_002185.5(IL7R):c.190_193dup (p.Asn65fs)Pathogenic
2734712NM_002185.5(IL7R):c.76C>T (p.Gln26Ter)Pathogenic
2734713NM_002185.5(IL7R):c.177del (p.Phe59fs)Pathogenic
2734714NM_002185.5(IL7R):c.493del (p.His165fs)Pathogenic
2734715NM_002185.5(IL7R):c.589_598del (p.Pro197fs)Pathogenic
2763597NM_002185.5(IL7R):c.80del (p.Asn27fs)Pathogenic
2780052NM_002185.5(IL7R):c.623del (p.Ile208fs)Pathogenic
2789689NM_002185.5(IL7R):c.538-2A>GPathogenic
2982246NM_002185.5(IL7R):c.752del (p.Phe251fs)Pathogenic
3068274NM_002185.5(IL7R):c.860del (p.Cys287fs)Pathogenic
3246329NC_000005.9:g.(?35860934)(35861112_?)delPathogenic
3246330NC_000005.9:g.(?35873562)(35876588_?)delPathogenic
353259NM_002185.5(IL7R):c.83-2A>TPathogenic
36392NM_002185.5(IL7R):c.353G>A (p.Cys118Tyr)Pathogenic

SpliceAI

1270 predictions. Top by Δscore:

VariantEffectΔscore
5:35860850:A:AGacceptor_gain1.0000
5:35860851:G:GGacceptor_gain1.0000
5:35860851:GGA:Gacceptor_gain1.0000
5:35860977:G:GTdonor_gain1.0000
5:35867304:A:AGacceptor_gain1.0000
5:35867304:AGT:Aacceptor_gain1.0000
5:35867304:AGTG:Aacceptor_gain1.0000
5:35867304:AGTGG:Aacceptor_gain1.0000
5:35867305:G:GGacceptor_gain1.0000
5:35867305:GTG:Gacceptor_gain1.0000
5:35867305:GTGG:Gacceptor_gain1.0000
5:35867305:GTGGG:Gacceptor_gain1.0000
5:35871051:TCCA:Tacceptor_loss1.0000
5:35871052:CCAG:Cacceptor_loss1.0000
5:35871054:A:AGacceptor_gain1.0000
5:35871054:A:Tacceptor_loss1.0000
5:35871055:G:GAacceptor_gain1.0000
5:35871055:GT:Gacceptor_gain1.0000
5:35871055:GTT:Gacceptor_gain1.0000
5:35871055:GTTA:Gacceptor_gain1.0000
5:35871055:GTTAA:Gacceptor_gain1.0000
5:35871147:G:GTdonor_gain1.0000
5:35871147:GAA:Gdonor_gain1.0000
5:35871150:G:GGdonor_gain1.0000
5:35875583:GAAAA:Gdonor_gain1.0000
5:35875588:G:GGdonor_gain1.0000
5:35876163:G:GTdonor_gain1.0000
5:35860849:CA:Cacceptor_loss0.9900
5:35860850:A:Cacceptor_loss0.9900
5:35860850:AG:Aacceptor_gain0.9900

AlphaMissense

3037 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:35873559:G:CR206P0.999
5:35873600:T:AW220R0.998
5:35873600:T:CW220R0.998
5:35873602:G:CW220C0.998
5:35873602:G:TW220C0.998
5:35873561:T:CS207P0.997
5:35873603:A:CS221R0.997
5:35873605:T:AS221R0.997
5:35873605:T:GS221R0.997
5:35873594:A:CS218R0.995
5:35873596:T:AS218R0.995
5:35873596:T:GS218R0.995
5:35860899:A:CS44R0.993
5:35860901:C:AS44R0.993
5:35860901:C:GS44R0.993
5:35871056:T:AV127D0.993
5:35871124:T:CF150L0.993
5:35871126:T:AF150L0.993
5:35871126:T:GF150L0.993
5:35873585:G:CG215R0.993
5:35860933:T:CL55P0.992
5:35860938:T:CC57R0.992
5:35873556:T:AV205D0.992
5:35860893:T:CC42R0.991
5:35873595:G:TS218I0.991
5:35871071:C:AP132H0.990
5:35871181:T:GY169D0.990
5:35860938:T:AC57S0.989
5:35860939:G:CC57S0.989
5:35871178:G:CA168P0.989

dbSNP variants (sampled 300 via entrez): RS1000047499 (5:35866630 T>A), RS1000140927 (5:35878629 A>C), RS1000195413 (5:35860207 G>A), RS1000207637 (5:35874490 T>A,G), RS1000269004 (5:35878833 TGAA>T), RS1000417037 (5:35866437 C>A,G), RS1000471252 (5:35863284 G>C), RS1000812835 (5:35873335 G>A), RS1000888959 (5:35870679 T>C), RS1001067467 (5:35875819 G>A), RS1001075840 (5:35861666 G>A), RS1001167284 (5:35876899 C>T), RS1001175902 (5:35855853 A>C,G,T), RS1001191563 (5:35862966 C>T), RS1001215074 (5:35877051 G>T)

Disease associations

OMIM: gene MIM:146661 | disease phenotypes: MIM:608971, MIM:612595, MIM:254500, MIM:603554

GenCC curated gene-disease

DiseaseClassificationInheritance
immunodeficiency 104DefinitiveAutosomal recessive
T-B+ severe combined immunodeficiency due to IL-7Ralpha deficiencySupportiveAutosomal recessive
Omenn syndromeSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
immunodeficiency 104DefinitiveAR

Mondo (7): immunodeficiency 104 (MONDO:0012163), T-B+ severe combined immunodeficiency due to IL-7Ralpha deficiency (MONDO:0015701), severe combined immunodeficiency (MONDO:0015974), breast neoplasm (MONDO:0021100), multiple sclerosis, susceptibility to, 3 (MONDO:0012957), plasma cell myeloma (MONDO:0009693), Omenn syndrome (MONDO:0011338)

Orphanet (5): T-B+ severe combined immunodeficiency due to IL-7Ralpha deficiency (Orphanet:169154), Severe combined immunodeficiency (Orphanet:183660), Multiple myeloma (Orphanet:29073), AL amyloidosis (Orphanet:85443), Omenn syndrome (Orphanet:39041)

HPO phenotypes

59 total (30 of 59 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000100Nephrotic syndrome
HP:0000155Oral ulcer
HP:0000388Otitis media
HP:0000403Recurrent otitis media
HP:0000821Hypothyroidism
HP:0000944Abnormal metaphysis morphology
HP:0000958Dry skin
HP:0000964Eczematoid dermatitis
HP:0000969Edema
HP:0000989Pruritus
HP:0001019Erythroderma
HP:0001072Thickened skin
HP:0001433Hepatosplenomegaly
HP:0001508Failure to thrive
HP:0001596Alopecia
HP:0001744Splenomegaly
HP:0001831Short toe
HP:0001875Decreased total neutrophil count
HP:0001880Increased total eosinophil count
HP:0001888Decreased total lymphocyte count
HP:0001903Anemia
HP:0001945Fever
HP:0001973Autoimmune thrombocytopenia
HP:0001974Increased total leukocyte count
HP:0002014Diarrhea
HP:0002020Gastroesophageal reflux
HP:0002028Chronic diarrhea
HP:0002090Pneumonia
HP:0002240Hepatomegaly

GWAS associations

43 associations (top):

StudyTraitp-value
GCST000038_8Type 1 diabetes8.000000e-06
GCST000062_6Multiple sclerosis3.000000e-07
GCST000424_9Multiple sclerosis2.000000e-06
GCST000949_1Multiple sclerosis4.000000e-07
GCST000964_43Ulcerative colitis4.000000e-08
GCST001010_2Primary biliary cholangitis1.000000e-11
GCST001198_25Multiple sclerosis2.000000e-08
GCST001685_1Primary biliary cholangitis4.000000e-08
GCST003129_22Primary biliary cholangitis5.000000e-11
GCST003184_13Atopic dermatitis2.000000e-10
GCST003184_5Atopic dermatitis3.000000e-14
GCST004145_4Primary biliary cholangitis6.000000e-09
GCST004627_62Lymphocyte count2.000000e-43
GCST004632_111Lymphocyte percentage of white cells3.000000e-29
GCST004633_53Neutrophil percentage of white cells2.000000e-19
GCST005038_42Allergic disease (asthma, hay fever or eczema)9.000000e-36
GCST005529_10Ankylosing spondylitis5.000000e-07
GCST005529_67Ankylosing spondylitis2.000000e-06
GCST005531_115Multiple sclerosis4.000000e-17
GCST005536_13Type 1 diabetes4.000000e-08
GCST005581_3Primary biliary cirrhosis2.000000e-13
GCST006409_29Allergic rhinitis4.000000e-32
GCST006585_1306Blood protein levels1.000000e-18
GCST007036_3Primary biliary cholangitis2.000000e-09
GCST007563_11Allergic disease (asthma, hay fever or eczema)3.000000e-15
GCST007564_36Asthma or allergic disease (pleiotropy)2.000000e-14
GCST007798_69Asthma2.000000e-13
GCST007799_44Asthma (adult onset)9.000000e-14
GCST007941_39Medication use (adrenergics, inhalants)9.000000e-10
GCST008916_32Asthma1.000000e-10

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0004267biliary liver cirrhosis
EFO:0004587lymphocyte count
EFO:0007993lymphocyte percentage of leukocytes
EFO:0007990neutrophil percentage of leukocytes
EFO:1002011adult onset asthma
EFO:0009941Inhalant adrenergic use measurement
EFO:0007992basophil percentage of leukocytes
EFO:0007989monocyte percentage of leukocytes

MeSH disease descriptors (4)

DescriptorNameTree numbers
D001943Breast NeoplasmsC04.588.180; C17.800.090.500
D009101Multiple MyelomaC04.557.595.500; C14.907.454.460; C15.378.147.780.650; C15.378.463.515.460; C20.683.515.845; C20.683.780.650
D016511Severe Combined ImmunodeficiencyC16.320.798.750; C16.614.815; C18.452.284.800; C20.673.795.750
C563822Severe Combined Immunodeficiency, Autosomal Recessive, T Cell Negative, B Cell Positive, NK Cell Positive (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs6897932IL7R0.000

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: catalytic receptor — IL-2 receptor family

Most potent curated ligand interactions (2 total), top 2:

LigandActionAffinityParameter
lusvertikimabAntagonist11.4pEC50
bempikibartBinding9.0pEC50

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases reaction, decreases expression, increases expression, affects binding8
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression, affects methylation6
bisphenol Adecreases expression, decreases methylation, increases expression3
Estradiolaffects expression, affects cotreatment, increases expression3
potassium chromate(VI)decreases expression, increases expression, affects cotreatment2
nickel sulfateincreases expression2
Bortezomibincreases expression, increases response to substance2
Arsenicincreases abundance, increases expression, affects expression, affects cotreatment2
Benzo(a)pyrenedecreases expression, increases expression2
Calcitrioldecreases expression2
Copperincreases expression, affects binding, decreases expression2
Nickelincreases expression2
Dronabinolincreases expression, decreases reaction2
Cadmium Chlorideincreases expression2
Nanotubes, Carbonincreases expression2
Glupearl 19Sincreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
captaxincreases expression1
geraniolincreases expression1
lead acetatedecreases expression1
trichostatin Aincreases expression1
cinnamaldehydeincreases expression1
arseniteaffects binding, decreases reaction1
afimoxifeneincreases expression1
butyraldehydeincreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
cobalt sulfateincreases expression1
4-hydroxy-2-nonenaldecreases expression1

Cellosaurus cell lines

6 cell lines: 4 cancer cell line, 2 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B8IIAbcam HCT 116 IL7R KOCancer cell lineMale
CVCL_B8XGAbcam MCF-7 IL7R KOCancer cell lineFemale
CVCL_B9KSAbcam A-549 IL7R KOCancer cell lineMale
CVCL_D9H7Ubigene HEK293 IL7R KOTransformed cell lineFemale
CVCL_E0F7Ubigene HeLa IL7R KOCancer cell lineFemale
CVCL_E8EIHEK-Blue IL-7Transformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00092183PHASE4COMPLETEDAn Investigational Drug for the Prevention of Chemotherapy-Induced Nausea and Vomiting (MK-0869-071)
NCT00128778PHASE4COMPLETEDMaintenance Treatment With Liposomal Doxorubicin (Caelyx) in Metastatic Breast Cancer Patients
NCT00302120PHASE4UNKNOWNThe MONET - Study: MR Mammography of Nonpalpable Breast Tumors
NCT00307606PHASE4UNKNOWNDoes a Single Steroid Injection Reduce the Formation of Postmastectomy Seroma
NCT00370240PHASE4COMPLETEDChlorhydrate of Ropivacaine and Breast Cancer Surgery
NCT00375752PHASE4TERMINATEDEfficacy and Safety of Letrozole vs. Letrozole Plus Zoledronic Acid as Endocrine Therapy Before Surgery in Postmenopausal Patients With Breast Cancer
NCT00575354PHASE4COMPLETEDComparison of Sevoflurane and Isoflurane Anesthesia for Benign Breast Tumor Excision
NCT00604968PHASE4TERMINATEDPegylated Liposomal Doxorubicin (Caelyx(R)) as Monotherapy in Elderly Patients With Locally Advanced and/or Metastatic Breast Cancer (Study P05059)
NCT00616135PHASE4COMPLETEDStudy of Autologous Fat Enhanced w/ Regenerative Cells Transplanted to Reconstruct Breast Deformities After Lumpectomy
NCT00649090PHASE4COMPLETEDA Study to Evaluate the Safety of Adjuvant Treatment With Exemestane Following Previous Treatment With Tamoxifen in Postmenopausal Women With Estrogen Sensitive Primary Breast Cancer
NCT00779285PHASE4TERMINATEDSafety Study of CAELYX in Patients With Metastatic Breast Cancer Previously Treated With Anthracyclines (Study P04057)(TERMINATED)
NCT01176916PHASE4COMPLETEDAromasin® Interventional Study Of Early Invasive Breast Cancer Patients In China
NCT01427400PHASE4UNKNOWNThe Use of Botulinum Toxin A in Two-Stage Tissue Expander/ Implant Breast Reconstruction
NCT01849380PHASE4UNKNOWNNeoadjuvant ECS Versus ECF in Local Advanced Breast Cancer
NCT01859936PHASE4COMPLETEDWill Preoperative MRI Breast in Women Under 56 Years With Breast Cancer Change Primary Treatment
NCT01948960PHASE4COMPLETEDInfluence of Exceptional Patient Characteristics on Everolimus Exposure
NCT01961544PHASE4COMPLETEDEribulin Mesylate Phase IV Clinical Trial in Korean Patients With Metastatic or Locally Advanced Breast Cancer
NCT01975064PHASE4COMPLETEDCancer and Anesthesia: Survival After Radical Surgery - a Comparison Between Propofol or Sevoflurane Anesthesia
NCT02004834PHASE4ACTIVE_NOT_RECRUITINGLevobupivacaine and Lidocaine for Paravertebral Block Causes Greater Hemodynamic Oscillations Than Levobupivacaine
NCT02372305PHASE4WITHDRAWNComparison of FlexHD and Alloderm Outcomes in Breast Reconstructive Surgery
NCT02479347PHASE4COMPLETEDWound Infections in Breast Cancer Surgery After Preoperative Skin Preparation With Chlorhexidine vs. Povidone-iodine
NCT02549677PHASE4COMPLETEDEpirubicin Versus Docetaxel Plus Cyclophosphamide in Lymph Node Negative, ER-positive, Her2-negative Breast Cancer
NCT02612870PHASE4UNKNOWNSienna+® Injection Time Study 4 Arms
NCT02627560PHASE4COMPLETEDThe Effect of Topical Tranexamic Acid on Bleeding and Seroma Formation in After Undergoing Mastectomy
NCT02661932PHASE4COMPLETEDFertility Preservation in Breast Cancer Patients
NCT02781259PHASE4UNKNOWNSelective Lymph Node Dissection Using Fluorescent Dye in Node-positive Breast Cancer
NCT02819921PHASE4TERMINATEDDesvenlafaxine for Treatment of Hot Flashes in Women With Breast Cancer Taking Tamoxifen
NCT03220178PHASE4TERMINATEDImpact of eHealth-support on Quality of Life in Metastatic Breast Cancer Patients Treated With Palbociclib and Endocrine Therapy
NCT03583944PHASE4COMPLETEDA Study to Evaluate Safety, Tolerability and Efficacy of Eribulin Mesylate in Treating Adult Females With Locally Advanced or Metastatic Breast Cancer
NCT03586154PHASE4COMPLETEDCombined Intra-articular Shoulder Injection and Stellate Ganglion Block in Chronic Post-mastectomy Shoulder Pain
NCT04707196PHASE4COMPLETEDA Study of Abemaciclib in Indian Women With Advanced Breast Cancer
NCT04931615PHASE4COMPLETEDARTISS a Single-centre Randomised Control Study
NCT05033769PHASE4UNKNOWNAssessing ImmunoResponse Post Eribulin: Eribulin and Immunogenicity in Advanced Breast Cancer
NCT05036005PHASE4UNKNOWNNeoadjuvant Ontruzant (SB3) in Patients With HER2-positive Early Breast Cancer: An Open-Label (NeoON)
NCT05452213PHASE4RECRUITINGComprehensive Analysis of Spatial, Temporal and Molecular Patterns of Ribociclib Efficacy and Resistance in Advanced Breast Cancer Patients
NCT05465031PHASE4RECRUITINGSacubitril/Valsartan in PriMAry preventIoN of the Cardiotoxicity of Systematic breaST canceR trEAtMent (MAINSTREAM)
NCT05949333PHASE4UNKNOWNReducing Neutropenia Incidence With Pegfilgrastim Administration on Day 3 After Chemotherapy
NCT07158164PHASE4RECRUITINGDPYD Pharmacogenomics and Fluoropyrimidine (FP) Dose-Adjustment
NCT07162259PHASE4NOT_YET_RECRUITINGCohort Study on Sequential ADC Therapy in HR-positive/HER2-negative Advanced Breast Cancer
NCT00220766PHASE3COMPLETEDRapid Infusion of Immune Globulin Intravenous (Human) In Primary Immunodeficiency Patients