SPDL1 (spindle apparatus coiled-coil protein 1)

Gene

• Entrez ID: 54908
• Gene name: Spindle apparatus coiled-coil protein 1
• Gene symbol: SPDL1
• Synonyms (NCBI Gene): CCDC99
• Chromosome: 5
• Chromosome location: 5q35.1
• Summary: This gene encodes a coiled-coil domain-containing protein that functions in mitotic spindle formation and chromosome segregation. The encoded protein plays a role in coordinating microtubule attachment by promoting recruitment of dynein proteins, and in m

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs730882228	CAAGCAAATTGGAAAAAGAAACTT>-	Likely-pathogenic	Inframe deletion, coding sequence variant, 3 prime UTR variant, genic downstream transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT004899	hsa-miR-124-3p	Microarray	15685193
MIRT004899	hsa-miR-124-3p	Microarray	18668037
MIRT121906	hsa-miR-543	HITS-CLIP	19536157
MIRT714875	hsa-miR-944	HITS-CLIP	19536157
MIRT714874	hsa-miR-4275	HITS-CLIP	19536157
MIRT121907	hsa-miR-1250-3p	HITS-CLIP	19536157
MIRT714873	hsa-miR-205-5p	HITS-CLIP	19536157
MIRT095945	hsa-miR-3143	HITS-CLIP	19536157
MIRT714872	hsa-miR-6868-3p	HITS-CLIP	19536157
MIRT440988	ebv-miR-BART13-3p	HITS-CLIP	22473208
MIRT440988	ebv-miR-BART13-3p	HITS-CLIP	22473208
MIRT121906	hsa-miR-543	HITS-CLIP	19536157
MIRT714875	hsa-miR-944	HITS-CLIP	19536157
MIRT714874	hsa-miR-4275	HITS-CLIP	19536157
MIRT121907	hsa-miR-1250-3p	HITS-CLIP	19536157
MIRT714873	hsa-miR-205-5p	HITS-CLIP	19536157
MIRT095945	hsa-miR-3143	HITS-CLIP	19536157
MIRT714872	hsa-miR-6868-3p	HITS-CLIP	19536157

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000132	Process	Establishment of mitotic spindle orientation	IBA
GO:0000132	Process	Establishment of mitotic spindle orientation	IMP	19468067
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000776	Component	Kinetochore	IEA
GO:0000922	Component	Spindle pole	IBA
GO:0000922	Component	Spindle pole	IDA	19468067
GO:0000922	Component	Spindle pole	IEA
GO:0000940	Component	Outer kinetochore	IBA
GO:0000940	Component	Outer kinetochore	IDA	19468067
GO:0000940	Component	Outer kinetochore	IEA
GO:0005515	Function	Protein binding	IPI	19468067, 25416956, 25910212, 26871637, 30258100, 33961781
GO:0005634	Component	Nucleus	IDA	19468067
GO:0005634	Component	Nucleus	IEA
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0007080	Process	Mitotic metaphase chromosome alignment	IBA
GO:0007080	Process	Mitotic metaphase chromosome alignment	IMP	19468067
GO:0007094	Process	Mitotic spindle assembly checkpoint signaling	IEA
GO:0016477	Process	Cell migration	IMP	30258100
GO:0019899	Function	Enzyme binding	IPI	23382074
GO:0034501	Process	Protein localization to kinetochore	IBA
GO:0034501	Process	Protein localization to kinetochore	IEA
GO:0034501	Process	Protein localization to kinetochore	IMP	19468067
GO:0043515	Function	Kinetochore binding	IBA
GO:0043515	Function	Kinetochore binding	IDA	19468067
GO:0043515	Function	Kinetochore binding	IEA
GO:0051301	Process	Cell division	IEA

Other IDs

• MIM: 616401
• HGNC: 26010
• e!Ensembl: ENSG00000040275

Protein

• UniProt ID: Q96EA4
• Protein name: Protein Spindly (hSpindly) (Arsenite-related gene 1 protein) (Coiled-coil domain-containing protein 99) (Rhabdomyosarcoma antigen MU-RMS-40.4A) (Spindle apparatus coiled-coil domain-containing protein 1)
• Protein function: Required for the localization of dynein and dynactin to the mitotic kintochore. Dynein is believed to control the initial lateral interaction between the kinetochore and spindle microtubules and to facilitate the subsequent formation of end-on k
• PDB: 8ARF
• Sequence:

  MEADIITNLRCRLKEAEEERLKAAQYGLQLVESQNELQNQLDKCRNEMMTMTESYEQEKY
  TLQREVELKSRMLESLSCECEAIKQQQKMHLEKLEEQLSRSHGQEVNELKTKIEKLKVEL
  DEARLSEKQLKHQVDHQKELLSCKSEELRVMSERVQESMSSEMLALQIELTEMESMKTTL
  KEEVNELQYRQEQLELLITNLMRQVDRLKEEKEEREKEAVSYYNALEKARVANQDLQVQL
  DQALQQALDPNSKGNSLFAEVEDRRAAMERQLISMKVKYQSLKKQNVFNREQMQRMKLQI
  ATLLQMKGSQTEFEQQERLLAMLEQKNGEIKHLLGEIRNLEKFKNLYDSMESKPSVDSGT
  LEDNTYYTDLLQMKLDNLNKEIESTKGELSIQRMKALFESQRALDIERKLFANERCLQLS
  ESENMKLRAKLDELKLKYEPEETVEVPVLKKRREVLPVDITTAKDACVNNSALGGEVYRL
  PPQKEETQSCPNSLEDNNLQLEKSVSIYTPVVSLSPHKNLPVDMQLKKEKKCVKLIGVPA
  DAEALSERSGNTPNSPRLAAESKLQTEVKEGKETSSKLEKETCKKLHPILYVSSKSTPET
  QCPQQ

• Sequence length: 605

Pathways

Reactome:

Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
Separation of Sister Chromatids
Resolution of Sister Chromatid Cohesion
RHO GTPases Activate Formins
Mitotic Prometaphase
EML4 and NUDC in mitotic spindle formation

Associated diseases

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
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Neonatal death	Likely pathogenic	rs730882228	RCV000162147	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe primary microcephaly	Likely pathogenic	rs730882228	RCV000162147	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEARING LOSS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC PULMONARY FIBROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTERSTITIAL LUNG DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PULMONARY FIBROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	30140263	Associate	★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune disease	Pubtator	32243638	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	37762557	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	31811111, 34478821	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	35184226	Associate	★☆☆☆☆ Found in Text Mining only
Colitis Ulcerative	Ulcerative colitis	Pubtator	37273534	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32577816, 35163739	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Hemidysplasia with Ichthyosiform Erythroderma and Limb Defects	Congenital hemidysplasia with ichthyosiform erythroderma and limb defects	Pubtator	34478821	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophageal neoplasm	Pubtator	39196978	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	39196978	Associate	★☆☆☆☆ Found in Text Mining only
Hepatitis Autoimmune	Autoimmune hepatitis	Pubtator	37102762	Associate	★☆☆☆☆ Found in Text Mining only
Hepatitis B	Hepatitis b	Pubtator	34478821	Associate	★☆☆☆☆ Found in Text Mining only
Hepatitis B Chronic	Hepatitis b	Pubtator	34478821	Stimulate	★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Idiopathic pulmonary fibrosis	Pubtator	33758299	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Immune System Diseases	Immune system disease	Pubtator	32243638	Associate	★☆☆☆☆ Found in Text Mining only
Intervertebral Disc Degeneration	Intervertebral disc disease	Pubtator	37915003	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Kidney neoplasm	Pubtator	35184226	Associate	★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis	Liver cirrhosis	Pubtator	34478821	Associate	★☆☆☆☆ Found in Text Mining only
Liver Cirrhosis Biliary	Liver cirrhosis	Pubtator	37915081	Stimulate	★☆☆☆☆ Found in Text Mining only
Liver Diseases	Liver disease	Pubtator	34478821	Associate	★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus Systemic	Systemic lupus erythematosus	Pubtator	32243638	Associate	★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	32493964	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	33233528	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	37762557	Associate	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	33306195	Associate	★☆☆☆☆ Found in Text Mining only