IGFLR1

Summary

IGFLR1 (IGF like family receptor 1, HGNC:23620) is a protein-coding gene on chromosome 19q13.12, encoding IGF-like family receptor 1 (Q9H665). Probable cell membrane receptor for the IGF-like family proteins.

Located in nucleoplasm and plasma membrane.

Source: NCBI Gene 79713 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 124 total
• Druggable target: yes
• MANE Select transcript: NM_024660

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23620
Approved symbol	IGFLR1
Name	IGF like family receptor 1
Location	19q13.12
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22573
Ensembl gene	ENSG00000126246
Ensembl biotype	protein_coding
OMIM	614143
Entrez	79713

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 23 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000246532, ENST00000586140, ENST00000587101, ENST00000588018, ENST00000588992, ENST00000589175, ENST00000591277, ENST00000591748, ENST00000592537, ENST00000592693, ENST00000592889, ENST00000871289, ENST00000871290, ENST00000871291, ENST00000871292, ENST00000871293, ENST00000871294, ENST00000871295, ENST00000871296, ENST00000871297, ENST00000929955, ENST00000929957, ENST00000966824, ENST00000966825, ENST00000966826, ENST00000966827, ENST00000966828

RefSeq mRNA: 5 — MANE Select: NM_024660 NM_001346003, NM_001346004, NM_001346005, NM_001346006, NM_024660

CCDS: CCDS12472, CCDS86751, CCDS86752

Canonical transcript exons

ENST00000246532 — 5 exons

Exon	Start	End
ENSE00001057198	35742396	35742452
ENSE00001276829	35741024	35741223
ENSE00003462473	35738801	35739626
ENSE00003584571	35739710	35740088
ENSE00003674314	35740380	35740564

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 97.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7923 / max 313.6844, expressed in 1606 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180547	11.9302	511
180546	2.9273	1174
180545	1.8588	782
180544	0.0760	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	97.34	gold quality
blood	UBERON:0000178	95.47	gold quality
monocyte	CL:0000576	95.36	gold quality
leukocyte	CL:0000738	95.24	gold quality
lymph node	UBERON:0000029	93.85	gold quality
vermiform appendix	UBERON:0001154	93.58	gold quality
spleen	UBERON:0002106	93.23	gold quality
right lobe of liver	UBERON:0001114	92.55	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.13	gold quality
bone marrow cell	CL:0002092	88.24	gold quality
liver	UBERON:0002107	87.65	gold quality
bone marrow	UBERON:0002371	86.53	gold quality
right adrenal gland	UBERON:0001233	85.72	gold quality
small intestine Peyer’s patch	UBERON:0003454	85.37	gold quality
small intestine	UBERON:0002108	84.30	gold quality
upper lobe of left lung	UBERON:0008952	84.15	gold quality
left adrenal gland	UBERON:0001234	84.09	gold quality
left adrenal gland cortex	UBERON:0035825	83.94	gold quality
tonsil	UBERON:0002372	83.47	gold quality
right adrenal gland cortex	UBERON:0035827	83.46	gold quality
mucosa of transverse colon	UBERON:0004991	82.93	gold quality
gall bladder	UBERON:0002110	82.70	gold quality
apex of heart	UBERON:0002098	82.21	gold quality
adrenal gland	UBERON:0002369	81.81	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.67	gold quality
metanephros cortex	UBERON:0010533	81.34	gold quality
right coronary artery	UBERON:0001625	81.31	gold quality
duodenum	UBERON:0002114	81.22	gold quality
adult mammalian kidney	UBERON:0000082	81.18	gold quality
right lobe of thyroid gland	UBERON:0001119	81.17	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	55.91
E-HCAD-6	yes	35.81
E-HCAD-11	yes	20.47
E-MTAB-9467	yes	16.10
E-CURD-112	yes	14.93
E-MTAB-6701	yes	14.61
E-MTAB-8410	yes	13.11
E-MTAB-9067	yes	12.45
E-CURD-122	yes	12.39
E-ANND-3	yes	8.92
E-CURD-88	yes	4.36
E-CURD-95	no	278.21

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

Literature-anchored findings (GeneRIF, showing 1)

• Murine insulin growth factor-like (IGFL) and human IGFL1 proteins are induced in inflammatory skin conditions and bind to a novel tumor necrosis factor receptor family member, IGFLR1. (PMID:21454693)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	igflr1	ENSDARG00000091650
mus_musculus	Igflr1	ENSMUSG00000036826
rattus_norvegicus	Igflr1	ENSRNOG00000020957

Protein

Protein identifiers

IGF-like family receptor 1 — Q9H665 (reviewed: Q9H665)

Alternative names: Transmembrane protein 149, U2 small nuclear RNA auxiliary factor 1-like 4

All UniProt accessions (7): Q9H665, K7EL86, K7EQI5, K7ES44, K7ESC2, S4R3Z9, U3KQL9

UniProt curated annotations — full annotation on UniProt →

Function. Probable cell membrane receptor for the IGF-like family proteins. Binds IGFL1 and IGFL3 with a higher affinity. May also bind IGFL2.

Subcellular location. Cell membrane.

Induction. Up-regulated by the pro-inflammatory cytokine TNFA and in skin upon tissue inflammation.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H665-1	1	yes
Q9H665-2	2

RefSeq proteins (5): NP_001332932, NP_001332933, NP_001332934, NP_001332935, NP_078936* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011029	DEATH-like_dom_sf	Homologous_superfamily
IPR042355	IGFLR1	Family

UniProt features (9 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H665-F1	72.73	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 220 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, MCLACHLAN_DENTAL_CARIES_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, AACYNNNNTTCCS_UNKNOWN, CREBP1_Q2, GGGTGGRR_PAX4_03, HATADA_METHYLATED_IN_LUNG_CANCER_DN, CREB_Q4, GATA3_01, ATF1_Q6, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, HNF4_DR1_Q3

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): nucleoplasm (GO:0005654), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
nuclear lumen	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1530 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IGFLR1	IGFL1	Q6UW32	615
IGFLR1	MDFIC2	A0A1B0GVS7	516
IGFLR1	IGFL3	Q6UXB1	505
IGFLR1	NRDE2	Q9H7Z3	461
IGFLR1	HBM	Q6B0K9	447
IGFLR1	IL18BP	O95998	418
IGFLR1	QRFPR	Q96P65	405
IGFLR1	CCDC160	A6NGH7	389
IGFLR1	RBM42	Q9BTD8	378
IGFLR1	FAM174C	Q9BVV8	366
IGFLR1	SLC25A53	Q5H9E4	363
IGFLR1	LIN37	Q96GY3	360
IGFLR1	IRAK1BP1	Q5VVH5	338
IGFLR1	SHISAL1	Q3SXP7	330
IGFLR1	CDK9	P50750	326

IntAct

9 interactions, top by confidence:

A	B	Type	Score
IGFL1	IGFLR1	psi-mi:“MI:0915”(physical association)	0.620
IGFLR1	IGFL1	psi-mi:“MI:0403”(colocalization)	0.620
IGFLR1	IGFL1	psi-mi:“MI:0915”(physical association)	0.620
N	NOP56	psi-mi:“MI:0914”(association)	0.530
IGFLR1	IGFL2	psi-mi:“MI:0915”(physical association)	0.400
IGFL3	IGFLR1	psi-mi:“MI:0915”(physical association)	0.400

ESM2 similar proteins: A0A5F4BST2, A5PJC7, A8MWV9, D3ZZP4, O14836, P0CAN6, P11911, P11912, P14753, Q01114, Q07303, Q13113, Q2KI80, Q2KL21, Q3TS39, Q3URD2, Q4V9L6, Q5F267, Q5FVJ4, Q5FVQ7, Q5RA41, Q5T1S8, Q6P9G4, Q6UWJ8, Q6UX34, Q80VJ8, Q810F0, Q86XR5, Q8BRJ3, Q8BX43, Q8K064, Q8K5A9, Q8N112, Q8N4K4, Q8N6L0, Q8NBR0, Q8NC24, Q8QZT4, Q8R138, Q923S2

Diamond homologs: A5PJC7, Q3U4N7, Q9H665

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	95
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

928 predictions. Top by Δscore:

Variant	Effect	Δscore
19:35739622:CAGTT:C	acceptor_gain	1.0000
19:35741133:C:CT	acceptor_gain	1.0000
19:35741234:C:CT	acceptor_gain	1.0000
19:35741235:G:T	acceptor_gain	1.0000
19:35741243:C:CT	acceptor_gain	1.0000
19:35741244:G:T	acceptor_gain	1.0000
19:35739624:GTT:G	acceptor_gain	0.9900
19:35739625:TTCTG:T	acceptor_loss	0.9900
19:35739626:TC:T	acceptor_loss	0.9900
19:35739627:C:CC	acceptor_gain	0.9900
19:35739627:CTG:C	acceptor_loss	0.9900
19:35739627:CTGGA:C	acceptor_loss	0.9900
19:35739628:T:A	acceptor_loss	0.9900
19:35741016:ATTCT:A	donor_loss	0.9900
19:35741018:TCTCA:T	donor_loss	0.9900
19:35741020:T:TC	donor_loss	0.9900
19:35741021:C:CC	donor_loss	0.9900
19:35741021:C:CG	donor_loss	0.9900
19:35741022:AC:A	donor_gain	0.9900
19:35741023:C:CT	donor_loss	0.9900
19:35741023:CC:C	donor_gain	0.9900
19:35741139:C:CT	acceptor_gain	0.9900
19:35741227:CA:C	acceptor_gain	0.9900
19:35741229:C:CC	acceptor_gain	0.9900
19:35741230:T:C	acceptor_gain	0.9900
19:35741234:C:T	acceptor_gain	0.9900
19:35741247:C:CT	acceptor_gain	0.9900
19:35739623:AGTT:A	acceptor_gain	0.9800
19:35739625:TT:T	acceptor_gain	0.9800
19:35739708:ACC:A	donor_gain	0.9800

AlphaMissense

2228 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:35740555:A:C	F56C	0.995
19:35740554:G:C	F56L	0.993
19:35740554:G:T	F56L	0.993
19:35740556:A:G	F56L	0.993
19:35739465:A:G	W295R	0.992
19:35739465:A:T	W295R	0.992
19:35739491:G:T	A286D	0.992
19:35741085:C:A	W32C	0.992
19:35741085:C:G	W32C	0.992
19:35739560:A:G	L263P	0.991
19:35739454:A:C	F298L	0.989
19:35739454:A:T	F298L	0.989
19:35739456:A:G	F298L	0.989
19:35740555:A:G	F56S	0.989
19:35740543:C:G	C60S	0.985
19:35740544:A:T	C60S	0.985
19:35741043:G:C	F46L	0.985
19:35741043:G:T	F46L	0.985
19:35741045:A:G	F46L	0.985
19:35741104:C:G	C26S	0.984
19:35741105:A:T	C26S	0.984
19:35739463:C:A	W295C	0.983
19:35739463:C:G	W295C	0.983
19:35739545:T:C	D268G	0.983
19:35739353:A:T	L332H	0.982
19:35739566:T:A	E261V	0.982
19:35741104:C:T	C26Y	0.982
19:35739560:A:T	L263Q	0.981
19:35739503:G:A	T282I	0.979
19:35739545:T:A	D268V	0.979

dbSNP variants (sampled 300 via entrez): RS1000971736 (19:35740802 G>A,T), RS1001911955 (19:35740214 G>A,T), RS1002970843 (19:35739116 C>G,T), RS1003090496 (19:35743423 G>A), RS1003120808 (19:35744197 G>A,T), RS1003632561 (19:35739852 T>A), RS1004310372 (19:35740248 C>T), RS1004951866 (19:35741715 G>A), RS1005034610 (19:35744258 C>T), RS1005277772 (19:35739501 G>A,C,T), RS1006039121 (19:35742666 C>A,T), RS1007034807 (19:35741480 C>T), RS1007555937 (19:35739372 C>G), RS1008033533 (19:35743039 G>A,C), RS1008111448 (19:35740628 C>A,G)

Disease associations

OMIM: gene MIM:614143 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST006585_1596	Blood protein levels	4.000000e-69
GCST010002_54	Refractive error	1.000000e-10
GCST010703_277	Brain morphology (MOSTest)	2.000000e-15
GCST90002404_531	Red cell distribution width	1.000000e-15

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2029192 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Nickel	increases expression	2
triphenyl phosphate	affects expression	1
terbufos	decreases methylation	1
arsenite	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	increases expression	1
Benzo(a)pyrene	increases methylation	1
Calcitriol	increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Dexamethasone	increases expression	1
Fonofos	decreases methylation	1
Estradiol	decreases expression	1
Hydrogen Peroxide	affects expression	1
Parathion	decreases methylation	1
Smoke	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases expression	1
Antirheumatic Agents	decreases expression	1
Copper Sulfate	decreases expression	1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL2033413	Binding	Inhibition of IGFR1 in human HEK293 cells after 1 hr by competition binding assay	Identification of 1-(3-(6,7-dimethoxyquinazolin-4-yloxy)phenyl)-3-(5-(1,1,1-trifluoro-2-methylpropan-2-yl)isoxazol-3-yl)urea hydrochloride (CEP-32496), a highly potent and orally efficacious inhibitor of V-RAF murine sarcoma viral oncogene homologue B1 (BRAF) V600E. — J Med Chem

Clinical trials (associated diseases)

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