IGDCC3

Summary

IGDCC3 (immunoglobulin superfamily DCC subclass member 3, HGNC:9700) is a protein-coding gene on chromosome 15q22.31, encoding Immunoglobulin superfamily DCC subclass member 3 (Q8IVU1).

Predicted to be involved in cell-cell adhesion. Predicted to act upstream of or within neuromuscular process controlling balance. Predicted to be located in membrane.

Source: NCBI Gene 9543 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 138 total
• MANE Select transcript: NM_004884

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9700
Approved symbol	IGDCC3
Name	immunoglobulin superfamily DCC subclass member 3
Location	15q22.31
Locus type	gene with protein product
Status	Approved
Aliases	HsT18880
Ensembl gene	ENSG00000174498
Ensembl biotype	protein_coding
OMIM	604184
Entrez	9543

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 17 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000327987, ENST00000558354, ENST00000559058, ENST00000559231, ENST00000559947, ENST00000863890, ENST00000863891, ENST00000920200, ENST00000920201, ENST00000920202, ENST00000920203, ENST00000920204, ENST00000920205, ENST00000920206, ENST00000920207, ENST00000920208, ENST00000920209, ENST00000920210, ENST00000920211

RefSeq mRNA: 1 — MANE Select: NM_004884 NM_004884

CCDS: CCDS10205

Canonical transcript exons

ENST00000327987 — 14 exons

Exon	Start	End
ENSE00001107357	65330550	65330741
ENSE00001107363	65330293	65330397
ENSE00001107373	65329390	65329597
ENSE00001200823	65329726	65329864
ENSE00001285942	65331050	65331214
ENSE00001305249	65334728	65334865
ENSE00001315405	65335291	65335421
ENSE00001321212	65327127	65329148
ENSE00001697589	65375097	65375402
ENSE00002713731	65377686	65378002
ENSE00003504266	65333257	65333415
ENSE00003553907	65331412	65331659
ENSE00003569452	65335812	65335956
ENSE00003587433	65331941	65332106

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 95.88.

FANTOM5 (CAGE): breadth broad, TPM avg 5.2097 / max 183.2942, expressed in 378 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150544	3.9107	344
150545	1.1716	234
150546	0.1229	75
150543	0.0046	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	95.88	gold quality
secondary oocyte	CL:0000655	95.81	gold quality
upper arm skin	UBERON:0004263	90.76	gold quality
kidney epithelium	UBERON:0004819	90.60	gold quality
buccal mucosa cell	CL:0002336	89.85	gold quality
cardiac muscle of right atrium	UBERON:0003379	89.45	gold quality
left ventricle myocardium	UBERON:0006566	87.72	gold quality
ganglionic eminence	UBERON:0004023	84.98	gold quality
tibialis anterior	UBERON:0001385	83.35	silver quality
ventral tegmental area	UBERON:0002691	83.13	gold quality
lateral nuclear group of thalamus	UBERON:0002736	82.87	gold quality
subthalamic nucleus	UBERON:0001906	81.78	gold quality
sperm	CL:0000019	81.30	silver quality
placenta	UBERON:0001987	80.62	gold quality
epithelial cell of pancreas	CL:0000083	80.47	gold quality
myocardium	UBERON:0002349	80.44	gold quality
dorsal plus ventral thalamus	UBERON:0001897	80.37	gold quality
cortical plate	UBERON:0005343	80.17	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.61	gold quality
lateral globus pallidus	UBERON:0002476	79.51	silver quality
inferior vagus X ganglion	UBERON:0005363	79.40	gold quality
substantia nigra pars compacta	UBERON:0001965	79.19	silver quality
deltoid	UBERON:0001476	79.03	silver quality
quadriceps femoris	UBERON:0001377	78.65	gold quality
nasal cavity epithelium	UBERON:0005384	78.33	gold quality
substantia nigra pars reticulata	UBERON:0001966	78.31	silver quality
cerebellar vermis	UBERON:0004720	77.76	gold quality
vastus lateralis	UBERON:0001379	77.69	gold quality
medulla oblongata	UBERON:0001896	77.66	gold quality
vena cava	UBERON:0004087	77.50	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-10018	yes	320.66
E-ANND-3	yes	2.59
E-GEOD-111727	no	452.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

133 targeting IGDCC3, 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-4262	100.00	73.26	3931
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-12136	99.98	72.81	5713
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	igdcc3	ENSDARG00000075158
mus_musculus	Igdcc3	ENSMUSG00000032394
rattus_norvegicus	Igdcc3	ENSRNOG00000030800

Paralogs (36): CNTN1 (ENSG00000018236), CDON (ENSG00000064309), NEO1 (ENSG00000067141), SDK2 (ENSG00000069188), IGSF9B (ENSG00000080854), IGSF9 (ENSG00000085552), NRCAM (ENSG00000091129), MXRA5 (ENSG00000101825), IGDCC4 (ENSG00000103742), CNTN3 (ENSG00000113805), IGSF21 (ENSG00000117154), CNTN6 (ENSG00000134115), CHL1 (ENSG00000134121), PTPRQ (ENSG00000139304), CNTN4 (ENSG00000144619), BOC (ENSG00000144857), SDK1 (ENSG00000146555), HMCN2 (ENSG00000148357), NCAM1 (ENSG00000149294), CNTN5 (ENSG00000149972), IGSF10 (ENSG00000152580), ROBO4 (ENSG00000154133), ROBO3 (ENSG00000154134), NCAM2 (ENSG00000154654), VCAM1 (ENSG00000162692), NFASC (ENSG00000163531), PRTG (ENSG00000166450), ROBO1 (ENSG00000169855), DSCAM (ENSG00000171587), VSIG10 (ENSG00000176834), DSCAML1 (ENSG00000177103), CNTN2 (ENSG00000184144), ROBO2 (ENSG00000185008), VSIG10L (ENSG00000186806), DCC (ENSG00000187323), L1CAM (ENSG00000198910)

Protein

Protein identifiers

Immunoglobulin superfamily DCC subclass member 3 — Q8IVU1 (reviewed: Q8IVU1)

Alternative names: Putative neuronal cell adhesion molecule

All UniProt accessions (3): Q8IVU1, H0YKK1, H0YNQ1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the immunoglobulin superfamily. DCC family.

RefSeq proteins (1): NP_004875* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF00041, PF07679, PF13927

UniProt features (28 total): glycosylation site 7, domain 6, disulfide bond 4, sequence conflict 4, region of interest 2, signal peptide 1, chain 1, compositionally biased region 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IVU1-F1	75.03	0.49

Functional residue map

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

Disulfide bonds (4): 63–117, 160–209, 259–307, 351–400

Glycosylation sites (7): 93, 246, 381, 382, 580, 604, 634

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 108 (showing top): CREL_01, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GOBP_NEUROMUSCULAR_PROCESS_CONTROLLING_BALANCE, GOBP_CELL_CELL_ADHESION, TCF4_Q5, GROSS_HYPOXIA_VIA_ELK3_UP, LEF1_Q6, IK3_01, GOBP_NEUROMUSCULAR_PROCESS, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, CERVERA_SDHB_TARGETS_2, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, WANG_CISPLATIN_RESPONSE_AND_XPC_UP, VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN, WANG_TNF_TARGETS

GO Biological Process (2): neuromuscular process controlling balance (GO:0050885), cell-cell adhesion (GO:0098609)

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
musculoskeletal movement	1
neuromuscular process	1
cell adhesion	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

828 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IGDCC3	UNC119	Q13432	738
IGDCC3	SIDT1	Q9NXL6	694
IGDCC3	VIM	P08670	650
IGDCC3	EBAG9	O00559	593
IGDCC3	MMP10	P09238	578
IGDCC3	KIF1A	Q12756	574
IGDCC3	CADPS	Q9ULU8	570
IGDCC3	UNC13B	O14795	567
IGDCC3	PTPN3	P26045	522
IGDCC3	FEZ1	Q99689	507
IGDCC3	PTGES	O14684	505
IGDCC3	AACS	Q86V21	474
IGDCC3	PHGDH	O43175	474
IGDCC3	ERI1	Q8IV48	470
IGDCC3	FN1	P02751	430

IntAct

9 interactions, top by confidence:

A	B	Type	Score
IGDCC3	WFIKKN2	psi-mi:“MI:0915”(physical association)	0.540
IGDCC3	WFIKKN2	psi-mi:“MI:0407”(direct interaction)	0.540
ICAM5	IGDCC3	psi-mi:“MI:0407”(direct interaction)	0.440
IGDCC3	LTF	psi-mi:“MI:0407”(direct interaction)	0.440
IGFBPL1	IGDCC3	psi-mi:“MI:0407”(direct interaction)	0.440
IGDCC3	IGFBP7	psi-mi:“MI:0407”(direct interaction)	0.440
IGDCC3	ILDR1	psi-mi:“MI:0915”(physical association)	0.400
CLEC4A	RBFOX3	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): IGDCC3 (Affinity Capture-MS), IGDCC3 (Affinity Capture-MS)

ESM2 similar proteins: A0JNA2, A4FUY1, C0HL12, O14514, O19131, O60241, O75325, P0C5H6, P15151, P32506, P32507, P70225, P98095, Q05BQ1, Q13477, Q14626, Q14CZ8, Q29RN8, Q3UHD1, Q4V9Z5, Q53EL9, Q5DRQ8, Q5R7Y0, Q5RF19, Q5STE3, Q63148, Q64385, Q6AX42, Q6BAA4, Q6MZW2, Q6UWL2, Q6UWL6, Q6UXD5, Q6WN34, Q7TSK2, Q7TSU7, Q8BHA1, Q8BQC3, Q8CGM1, Q8IVU1

Diamond homologs: A0A1Y9G8H0, A0A452E9Y6, A1KZ92, A2A8L5, A2AJ76, A4IFW2, A4IGL7, A4IIW9, A5JUY8, A7MBJ4, A8WGA3, A8WQH2, B0BNK7, B3A0P3, D2HFT7, D3YXG0, D4A1J9, D4ABX8, G5EBF1, G5EG78, H2A0M7, O15146, O35158, O55005, O89026, P05164, P07202, P09933, P0C6S8, P0C7J6, P11247, P11678, P14650, P16621, P22079, P23468, P35419, P49290, P70193, P80025

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	123
Likely benign	4
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2951 predictions. Top by Δscore:

Variant	Effect	Δscore
15:65329385:CTCA:C	donor_gain	1.0000
15:65329386:TCA:T	donor_loss	1.0000
15:65329387:CA:C	donor_loss	1.0000
15:65329388:A:AC	donor_gain	1.0000
15:65329388:ACT:A	donor_loss	1.0000
15:65329389:C:CG	donor_gain	1.0000
15:65329389:CT:C	donor_gain	1.0000
15:65329389:CTG:C	donor_gain	1.0000
15:65329389:CTGT:C	donor_gain	1.0000
15:65329389:CTGTG:C	donor_gain	1.0000
15:65329610:C:CT	acceptor_gain	1.0000
15:65329610:C:T	acceptor_gain	1.0000
15:65329611:A:T	acceptor_gain	1.0000
15:65329616:T:C	acceptor_gain	1.0000
15:65329616:T:TC	acceptor_gain	1.0000
15:65329724:ACCTG:A	donor_gain	1.0000
15:65329725:CCTGC:C	donor_gain	1.0000
15:65329728:G:A	donor_gain	1.0000
15:65329860:CAAGG:C	acceptor_gain	1.0000
15:65329861:AAGG:A	acceptor_gain	1.0000
15:65329862:AGG:A	acceptor_gain	1.0000
15:65329863:GG:G	acceptor_gain	1.0000
15:65329864:GC:G	acceptor_loss	1.0000
15:65329865:C:CC	acceptor_gain	1.0000
15:65329865:CTGG:C	acceptor_loss	1.0000
15:65330287:CCTCA:C	donor_loss	1.0000
15:65330288:CTCAC:C	donor_loss	1.0000
15:65330289:TCA:T	donor_loss	1.0000
15:65330290:CA:C	donor_loss	1.0000
15:65330291:ACCTG:A	donor_loss	1.0000

AlphaMissense

5197 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:65332000:C:A	W363C	1.000
15:65332000:C:G	W363C	1.000
15:65332043:A:G	F349S	1.000
15:65333364:A:G	L292P	1.000
15:65334738:C:A	W271C	1.000
15:65334738:C:G	W271C	1.000
15:65334740:A:G	W271R	1.000
15:65334740:A:T	W271R	1.000
15:65335850:C:A	W172C	1.000
15:65335850:C:G	W172C	1.000
15:65335852:A:G	W172R	1.000
15:65335852:A:T	W172R	1.000
15:65330370:A:G	L594P	0.999
15:65331476:C:A	W444C	0.999
15:65331476:C:G	W444C	0.999
15:65331478:A:G	W444R	0.999
15:65331478:A:T	W444R	0.999
15:65331564:A:G	L415P	0.999
15:65331596:G:C	N404K	0.999
15:65331596:G:T	N404K	0.999
15:65331616:A:C	Y398D	0.999
15:65331654:A:G	L385P	0.999
15:65332002:A:G	W363R	0.999
15:65332002:A:T	W363R	0.999
15:65332043:A:C	F349C	0.999
15:65333268:A:G	L324P	0.999
15:65333318:A:C	C307W	0.999
15:65333319:C:T	C307Y	0.999
15:65333320:A:G	C307R	0.999
15:65333325:T:C	Y305C	0.999

dbSNP variants (sampled 300 via entrez): RS1000014601 (15:65350185 G>A), RS1000039593 (15:65340481 C>G,T), RS1000063700 (15:65364298 G>A), RS1000095218 (15:65334548 C>T), RS1000204136 (15:65377909 G>A,C,T), RS1000216703 (15:65361845 A>G), RS1000237436 (15:65346417 T>C), RS1000264556 (15:65328755 G>A,C,T), RS1000351334 (15:65373373 G>A), RS1000417735 (15:65346127 T>C), RS1000435843 (15:65367759 G>T), RS1000459287 (15:65358911 C>T), RS1000507356 (15:65337933 G>T), RS1000550944 (15:65377058 C>A), RS1000568992 (15:65361608 C>G,T)

Disease associations

OMIM: gene MIM:604184 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases expression	5
trichostatin A	affects cotreatment, increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression	3
sodium arsenite	affects binding, increases reaction, decreases expression	2
Panobinostat	increases expression, affects cotreatment	2
Estradiol	decreases expression	2
Tretinoin	increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
bisphenol A	affects expression	1
beta-lapachone	decreases expression	1
methylparaben	increases expression	1
butyraldehyde	increases expression	1
aflatoxin B2	increases methylation	1
butylparaben	increases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
theaflavin-3,3’-digallate	affects expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Arbutin	decreases expression	1
Atrazine	increases expression	1
Azathioprine	decreases expression	1
Lead	affects expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Quercetin	decreases expression	1
Rotenone	decreases expression	1
Dronabinol	increases expression	1
Thimerosal	decreases expression	1

Clinical trials (associated diseases)

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