IGFL3

Summary

IGFL3 (IGF like family member 3, HGNC:32930) is a protein-coding gene on chromosome 19q13.32, encoding Insulin growth factor-like family member 3 (Q6UXB1). Potential ligand of the IGFLR1 cell membrane receptor.

IGFL3 belongs to the insulin-like growth factor (IGF; see MIM 147440) family of signaling molecules that play critical roles in cellular energy metabolism and in growth and development, especially prenatal growth (Emtage et al., 2006 [PubMed 16890402]).

Source: NCBI Gene 388555 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_207393

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32930
Approved symbol	IGFL3
Name	IGF like family member 3
Location	19q13.32
Locus type	gene with protein product
Status	Approved
Aliases	UNQ483
Ensembl gene	ENSG00000188624
Ensembl biotype	protein_coding
OMIM	610546
Entrez	388555

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000341415

RefSeq mRNA: 1 — MANE Select: NM_207393 NM_207393

CCDS: CCDS33058

Canonical transcript exons

ENST00000341415 — 4 exons

Exon	Start	End
ENSE00001367460	46124625	46124688
ENSE00001374757	46124268	46124321
ENSE00001381919	46123886	46124156
ENSE00001389450	46120067	46120357

Expression profiles

Bgee: expression breadth broad, 74 present calls, max score 85.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.3834 / max 623.9075, expressed in 113 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181613	1.3757	110
181614	0.0077	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	85.90	gold quality
zone of skin	UBERON:0000014	85.27	gold quality
skin of abdomen	UBERON:0001416	84.57	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.20	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.17	gold quality
corpus callosum	UBERON:0002336	63.94	gold quality
sural nerve	UBERON:0015488	62.04	gold quality
smooth muscle tissue	UBERON:0001135	48.26	gold quality
mucosa of transverse colon	UBERON:0004991	43.58	silver quality
duodenum	UBERON:0002114	41.30	gold quality
right lung	UBERON:0002167	40.94	silver quality
right uterine tube	UBERON:0001302	40.83	silver quality
stromal cell of endometrium	CL:0002255	40.74	silver quality
myometrium	UBERON:0001296	39.10	gold quality
mucosa of stomach	UBERON:0001199	38.62	silver quality
muscle tissue	UBERON:0002385	38.62	gold quality
right adrenal gland cortex	UBERON:0035827	37.30	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
skeletal muscle tissue	UBERON:0001134	36.21	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
monocyte	CL:0000576	35.80	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
cortex of kidney	UBERON:0001225	35.22	silver quality
testis	UBERON:0000473	35.09	silver quality
leukocyte	CL:0000738	35.06	silver quality
right atrium auricular region	UBERON:0006631	34.93	silver quality
left testis	UBERON:0004533	34.81	silver quality
multicellular organism	UBERON:0000468	34.74	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting IGFL3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-346	97.01	66.97	662
HSA-MIR-2276-5P	96.27	65.85	937
HSA-MIR-6796-5P	95.37	66.08	1120

Literature-anchored findings (GeneRIF, showing 1)

• IGFL3 expression is significantly downregulated in human masticatory mucosa during wound healing (PMID:28005267)

Cross-species orthologs

0 orthologs

Paralogs (3): IGFL1 (ENSG00000188293), IGFL2 (ENSG00000204866), IGFL4 (ENSG00000204869)

Protein

Protein identifiers

Insulin growth factor-like family member 3 — Q6UXB1 (reviewed: Q6UXB1)

All UniProt accessions (1): Q6UXB1

UniProt curated annotations — full annotation on UniProt →

Function. Potential ligand of the IGFLR1 cell membrane receptor.

Subcellular location. Secreted.

Tissue specificity. Detected in the cerebellum.

Similarity. Belongs to the IGFL family.

RefSeq proteins (1): NP_997276* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032744	IGFL	Family

Pfam: PF14653

UniProt features (3 total): signal peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXB1-F1	76.07	0.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): OCT1_03, GOMF_SIGNALING_RECEPTOR_BINDING, NKX3A_01, MIR4447, MIR4472, MEBARKI_HCC_PROGENITOR_WNT_UP, MEBARKI_HCC_PROGENITOR_WNT_UP_CTNNB1_DEPENDENT, chr19q13, GSE6674_UNSTIM_VS_CPG_STIM_BCELL_UP, KONDO_PROSTATE_CANCER_WITH_H3K27ME3, GSE20727_DNFB_ALLERGEN_VS_ROS_INH_AND_DNFB_ALLERGEN_TREATED_DC_UP, GSE40493_BCL6_KO_VS_WT_TREG_DN

GO Biological Process (0):

GO Molecular Function (1): signaling receptor binding (GO:0005102)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

170 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IGFL3	B3KSW5	B3KSW5	583
IGFL3	IGFLR1	Q9H665	505
IGFL3	ZSWIM4	Q9H7M6	348
IGFL3	SYT16	Q17RD7	348
IGFL3	IGFBPL1	Q8WX77	346
IGFL3	FXYD7	P58549	322
IGFL3	SIAH3	Q8IW03	322
IGFL3	FIBCD1	Q8N539	313
IGFL3	PLGLB1	Q02325	302
IGFL3	ARSJ	Q5FYB0	300
IGFL3	GPR15LG	Q6UWK7	294
IGFL3	GIMAP8	Q8ND71	290
IGFL3	MAGEA9B	P43362	271
IGFL3	PLAAT1	Q9HDD0	269
IGFL3	ATE1	O95260	247
IGFL3	S100P	P25815	247

IntAct

3 interactions, top by confidence:

A	B	Type	Score
IGFL3	IGFLR1	psi-mi:“MI:0915”(physical association)	0.400
IGFL3	CBX4	psi-mi:“MI:0914”(association)	0.350

BioGRID (74): LRP5 (Affinity Capture-MS), SORL1 (Affinity Capture-MS), LAMA1 (Affinity Capture-MS), MICA (Affinity Capture-MS), NOTCH3 (Affinity Capture-MS), AGRN (Affinity Capture-MS), ADAM11 (Affinity Capture-MS), B4GALT1 (Affinity Capture-MS), JAG2 (Affinity Capture-MS), PLXNA2 (Affinity Capture-MS), CACNA2D1 (Affinity Capture-MS), LRP12 (Affinity Capture-MS), CBX4 (Affinity Capture-MS), ATRN (Affinity Capture-MS), SPRYD3 (Affinity Capture-MS)

ESM2 similar proteins: A2BDC9, A4IFM1, A4IHZ3, B1AL88, B4DS77, E7F5F0, E7FAP8, F8W2C9, O35181, O62647, P12272, P13085, P13385, P17251, P22858, P25308, P43145, P51864, P52211, P56975, P58073, P97297, P97766, Q02816, Q13361, Q28022, Q2YDG7, Q4RU86, Q4V9H3, Q5PQX1, Q60485, Q62923, Q640B5, Q64387, Q6B9Z1, Q6INW9, Q6P1H6, Q6UWQ7, Q6UXB1, Q6UXQ4

Diamond homologs: Q6B9Z0, Q6B9Z1, Q6UW32, Q6UWQ7, Q6UXB1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

766 predictions. Top by Δscore:

Variant	Effect	Δscore
19:46121454:A:AC	donor_gain	0.9900
19:46121454:ACT:A	donor_gain	0.9900
19:46121455:C:CC	donor_gain	0.9900
19:46121455:CTC:C	donor_gain	0.9900
19:46121466:ATAG:A	donor_gain	0.9900
19:46123308:T:C	acceptor_gain	0.9900
19:46124262:CCTTA:C	donor_loss	0.9900
19:46124263:CTTA:C	donor_loss	0.9900
19:46124264:TTA:T	donor_loss	0.9900
19:46124265:TA:T	donor_loss	0.9900
19:46121532:C:CC	acceptor_gain	0.9800
19:46124619:A:AC	donor_gain	0.9800
19:46124620:C:CC	donor_gain	0.9800
19:46121528:TCAGC:T	acceptor_loss	0.9600
19:46121529:CAG:C	acceptor_gain	0.9600
19:46121529:CAGCT:C	acceptor_loss	0.9600
19:46121530:AGC:A	acceptor_loss	0.9600
19:46121531:GC:G	acceptor_loss	0.9600
19:46121532:C:CA	acceptor_loss	0.9600
19:46121533:T:G	acceptor_loss	0.9600
19:46123304:CATCT:C	acceptor_gain	0.9600
19:46121530:AG:A	acceptor_gain	0.9500
19:46123307:C:CC	acceptor_gain	0.9500
19:46121455:CT:C	donor_gain	0.9400
19:46121468:AG:A	donor_gain	0.9400
19:46121527:CTCAG:C	acceptor_gain	0.9400
19:46124185:C:CT	acceptor_gain	0.9300
19:46121528:TCAG:T	acceptor_gain	0.9200
19:46121529:CAGC:C	acceptor_gain	0.9200
19:46121534:G:C	acceptor_gain	0.9200

AlphaMissense

802 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:46124011:G:C	F75L	0.937
19:46124011:G:T	F75L	0.937
19:46124013:A:G	F75L	0.937
19:46124008:C:A	W76C	0.934
19:46124008:C:G	W76C	0.934
19:46123957:A:C	F93L	0.922
19:46123957:A:T	F93L	0.922
19:46123959:A:G	F93L	0.922
19:46124000:A:C	F79C	0.908
19:46124075:C:G	C54S	0.908
19:46124076:A:T	C54S	0.908
19:46124012:A:C	F75C	0.895
19:46124072:C:G	C55S	0.894
19:46124073:A:T	C55S	0.894
19:46124108:C:G	C43S	0.880
19:46124109:A:T	C43S	0.880
19:46124076:A:G	C54R	0.875
19:46123975:A:C	F87L	0.867
19:46123975:A:T	F87L	0.867
19:46123977:A:G	F87L	0.867
19:46123991:C:G	C82S	0.867
19:46123992:A:T	C82S	0.867
19:46124002:G:C	C78W	0.863
19:46124030:C:G	C69S	0.863
19:46124031:A:T	C69S	0.863
19:46124094:A:C	Y48D	0.861
19:46123935:C:A	G101C	0.856
19:46123958:A:C	F93C	0.856
19:46124071:A:C	C55W	0.848
19:46123992:A:G	C82R	0.847

dbSNP variants (sampled 300 via entrez): RS1000259991 (19:46122517 C>T), RS1000953312 (19:46125678 A>C), RS1001364786 (19:46125274 C>G), RS1001410496 (19:46125089 T>G), RS1001534450 (19:46120887 C>T), RS1002180468 (19:46124763 G>A), RS1002694365 (19:46124362 T>C), RS1003235576 (19:46119766 G>A), RS1003750777 (19:46123644 G>T), RS1004776583 (19:46122969 G>T), RS1005554426 (19:46125756 C>T), RS1005794518 (19:46121517 A>G), RS1006041615 (19:46121349 A>G,T), RS1006082333 (19:46125014 A>G), RS1006161260 (19:46121844 T>C,G)

Disease associations

OMIM: gene MIM:610546 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenate	decreases expression, increases abundance	1
sodium arsenite	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
jinfukang	affects cotreatment, increases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	increases expression	1
Vehicle Emissions	decreases expression, decreases reaction	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Particulate Matter	decreases reaction, decreases expression	1

Clinical trials (associated diseases)

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