DLL3 (delta like canonical Notch ligand 3)

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Gene Gene information from NCBI Gene database.
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Entrez ID 10683
Gene name Delta like canonical Notch ligand 3
Gene symbol DLL3
Synonyms (NCBI Gene)
SCDO1
Chromosome 19
Chromosome location 19q13.2
Summary This gene encodes a member of the delta protein ligand family. This family functions as Notch ligands that are characterized by a DSL domain, EGF repeats, and a transmembrane domain. Mutations in this gene cause autosomal recessive spondylocostal dysostos
SNPs SNP information provided by dbSNP.
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SNP ID Visualize variation Clinical significance Consequence
rs104894674 G>A Pathogenic Coding sequence variant, missense variant
rs104894675 C>T Pathogenic Coding sequence variant, stop gained
rs104894676 G>A Pathogenic, likely-pathogenic Coding sequence variant, missense variant
rs200275281 C>G,T Pathogenic Missense variant, coding sequence variant, stop gained
rs771875570 C>A Pathogenic Coding sequence variant, stop gained
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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GO ID Ontology Definition Evidence Reference
GO:0001501 Process Skeletal system development IEA
GO:0001501 Process Skeletal system development IMP 10742114
GO:0001756 Process Somitogenesis IEA
GO:0005112 Function Notch binding IBA
GO:0005112 Function Notch binding NAS 10742114
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
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MIM HGNC e!Ensembl
602768 2909 ENSG00000090932
Protein Protein information from UniProt database.
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UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NYJ7
Protein name Delta-like protein 3 (Drosophila Delta homolog 3) (Delta3)
Protein function Inhibits primary neurogenesis. May be required to divert neurons along a specific differentiation pathway. Plays a role in the formation of somite boundaries during segmentation of the paraxial mesoderm (By similarity).
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00008 EGF 316 → 349 EGF-like domain Domain
PF00008 EGF 357 → 387 EGF-like domain Domain
PF00008 EGF 278 → 308 EGF-like domain Domain
PF00008 EGF 395 → 425 EGF-like domain Domain
PF12661 hEGF 438 → 459 Human growth factor-like EGF Domain
Sequence 
MVSPRMSGLLSQTVILALIFLPQTRPAGVFELQIHSFGPGPGPGAPRSPCSARLPCRLFF
RVCLKPGLSEEAAESPCALGAALSARGPVYTEQPGAPAPDLPLPDGLLQVPFRDAWPGTF
SFIIETWREELGDQIGGPAWSLLARVAGRRRLAAGGPWARDIQRAGAWELRFSYRARCEP
PAVGTACTRLCRPRSAPSRCGPGLRPCAPLEDECEAPLVCRAGCSPEHGFCEQPGECRCL
EGWTGPLCTVPVSTSSCLSPRGPSSATTGCLVPGPGPCDGNPCANGGSCSETPRSFECTC
PRGFYGLRCEVSGVTCADGPCFNGGLCVGGADPDSAYICHCPPGFQGSNCEKRVDRCSLQ
PCRNGGLCLDLGHALRCRCRAGFAGPRCEHDLDDCAGRACANGGTCVEGGGAHRCSCALG
FGGRDCRERADPCAARPCAHGGRCYAHFSGLVCACAPGYMGARCEFPVHPDGASALPAAP
PGLRPGDPQRYLLPPALGLLVAAGVAGAALLLVHVRRRGHSQDAGSRLLAGTPEPSVHAL
PDALNNLRTQEGSGDGPSSSVDWNRPEDVDPQGIYVISAPSIYAREVATPLFPPLHTGRA
GQRQHLLFPYPSSILSVK
Sequence length 618
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
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KEGG Pathway
Endocrine resistance
Notch signaling pathway
Th1 and Th2 cell differentiation
Pathways in cancer
Chemical carcinogenesis - receptor activation
Breast cancer
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
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Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
DLL3-related disorder Likely pathogenic; Pathogenic rs1452482256 RCV003392559
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hemivertebrae Pathogenic rs200275281 RCV001257369
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Rib fusion Pathogenic rs200275281 RCV001257369
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spondylocostal dysostosis 1, autosomal recessive Likely pathogenic; Pathogenic rs2079604821, rs2144761828, rs2514649158, rs786205519, rs786200900, rs777791545, rs786200902, rs104894675, rs786200903, rs104894676, rs888371213, rs1261285510, rs752277223, rs962071242, rs2514643690
View all (3 more)		 RCV001780936
RCV001806346
RCV002283621
RCV001328972
RCV000007231
View all (13 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Show/Hide Unknown Diseases (20)
Phenotype Name Clinical Significance Source Reference Evidence Score
ASTROCYTOMA — CTD 21127729
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE SPONDYLOCOSTAL DYSOSTOSIS — CTD, Orphanet
CTD, Orphanet 		20301771, 20301771
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL ABNORMALITIES — CTD 17849441
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CONGENITAL ABNORMALITY — Disgenet —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Show/Hide Text Mining Associations (109)
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acquired Kyphoscoliosis Acquired Kyphoscoliosis HPO_DG
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 30894499
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 27196489
★★★★★
★☆☆☆☆
Found in Text Mining only
Anaplastic astrocytoma Anaplastic Astrocytoma CTD_human_DG 21127729
★★★★★
★☆☆☆☆
Found in Text Mining only
Anemia, Sickle Cell Anemia BEFREE 12141422, 15122512, 21147753
★★★★★
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 22190977 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Asthma Asthma BEFREE 30843783
★★★★★
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma CTD_human_DG 21127729
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★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autosomal recessive spondylocostal dysostosis Spondylocostal Dysostosis Orphanet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Breast Carcinoma Breast Carcinoma BEFREE 16501043
★★★★★
★☆☆☆☆
Found in Text Mining only
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LFNG 2 shared diseasesSpondylocostal dysostosis, Jarcho-levin syndrome 1 shared pathwayNotch signaling pathway 6 shared evidence sourcesDisgenet (Spondylocostal dysostosis), Orphanet (Spondylocostal dysostosis), CTD (Spondylocostal dysostosis), Disgenet (Jarcho-levin syndrome), ClinVar (Spondylocostal dysostosis), HPO (Spondylocostal dysostosis) Related via 2 shared diseases including Spondylocostal dysostosis, Jarcho-levin syndrome — evidence mostly Disgenet. JAG2 2 shared diseasesCraniofacial abnormalities, Syndactyly 4 shared pathwaysEndocrine resistance, Notch signaling pathway, Th1 and Th2 cell differentiation, Breast cancer 3 shared evidence sourcesCTD (Craniofacial abnormalities), Disgenet (Craniofacial abnormalities), Disgenet (Syndactyly) Related via 4 shared pathways including Endocrine resistance, Notch signaling pathway — evidence mostly Disgenet. HES7 2 shared diseasesSpondylocostal dysostosis, Jarcho-levin syndrome 6 shared evidence sourcesDisgenet (Spondylocostal dysostosis), Orphanet (Spondylocostal dysostosis), CTD (Spondylocostal dysostosis), Disgenet (Jarcho-levin syndrome), ClinVar (Spondylocostal dysostosis), HPO (Spondylocostal dysostosis) Related via 2 shared diseases including Spondylocostal dysostosis, Jarcho-levin syndrome — evidence mostly Disgenet. RIPPLY2 2 shared diseasesSpondylocostal dysostosis, Jarcho-levin syndrome 6 shared evidence sourcesDisgenet (Spondylocostal dysostosis), Orphanet (Spondylocostal dysostosis), CTD (Spondylocostal dysostosis), Disgenet (Jarcho-levin syndrome), ClinVar (Spondylocostal dysostosis), HPO (Spondylocostal dysostosis) Related via 2 shared diseases including Spondylocostal dysostosis, Jarcho-levin syndrome — evidence mostly Disgenet. TBX6 2 shared diseasesSpondylocostal dysostosis, Jarcho-levin syndrome 7 shared evidence sourcesDisgenet (Spondylocostal dysostosis), Orphanet (Spondylocostal dysostosis), CTD (Spondylocostal dysostosis), Disgenet (Jarcho-levin syndrome), Disgenet (Scoliosis), ClinVar (Spondylocostal dysostosis), HPO (Spondylocostal dysostosis) Related via 2 shared diseases including Spondylocostal dysostosis, Jarcho-levin syndrome — evidence mostly Disgenet.
Hypertension Linked via 2 of 5 related genesLFNG, HES7 Cardiovascular disease Linked via 1 of 5 related genesLFNG Limb girdle muscular dystrophy Linked via 1 of 5 related genesJAG2 Breast neoplasms Linked via 1 of 5 related genesJAG2 Pancreatic ductal carcinoma Linked via 1 of 5 related genesJAG2