TUBGCP2 (tubulin gamma complex component 2)

Gene

• Entrez ID: 10844
• Gene name: Tubulin gamma complex component 2
• Gene symbol: TUBGCP2
• Synonyms (NCBI Gene): ALP4, GCP-2, GCP2, Grip103, PAMDDFS, SPBC97, SPC97, Spc97p, h103p, hGCP2, hSpc97
• Chromosome: 10
• Chromosome location: 10q26.3

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs34832477	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, non coding transcript variant
rs200129338	G>A	Uncertain-significance, pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1449999247	C>G	Pathogenic, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs1589822227	T>C	Pathogenic	Splice acceptor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT030509	hsa-miR-24-3p	Microarray	19748357
MIRT032408	hsa-let-7b-5p	Proteomics	18668040
MIRT051231	hsa-miR-16-5p	CLASH	23622248
MIRT049523	hsa-miR-92a-3p	CLASH	23622248
MIRT044719	hsa-miR-320a	CLASH	23622248
MIRT1463559	hsa-miR-3667-3p	CLIP-seq
MIRT1463560	hsa-miR-4421	CLIP-seq
MIRT2139325	hsa-miR-3074-5p	CLIP-seq
MIRT2139326	hsa-miR-370	CLIP-seq
MIRT2139327	hsa-miR-4705	CLIP-seq
MIRT2139328	hsa-miR-518a-5p	CLIP-seq
MIRT2139329	hsa-miR-527	CLIP-seq
MIRT2139330	hsa-miR-548g	CLIP-seq
MIRT2360090	hsa-miR-1179	CLIP-seq
MIRT2139328	hsa-miR-518a-5p	CLIP-seq
MIRT2139329	hsa-miR-527	CLIP-seq
MIRT2139330	hsa-miR-548g	CLIP-seq
MIRT2139328	hsa-miR-518a-5p	CLIP-seq
MIRT2139329	hsa-miR-527	CLIP-seq
MIRT2139328	hsa-miR-518a-5p	CLIP-seq
MIRT2139329	hsa-miR-527	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000226	Process	Microtubule cytoskeleton organization	IEA
GO:0000278	Process	Mitotic cell cycle	IBA
GO:0000922	Component	Spindle pole	IEA
GO:0000930	Component	Gamma-tubulin complex	IBA
GO:0001764	Process	Neuron migration	IMP	31630790
GO:0005515	Function	Protein binding	IPI	16980960, 26213385, 32296183
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	21399614
GO:0005813	Component	Centrosome	IEA
GO:0005815	Component	Microtubule organizing center	IDA	9566967
GO:0005815	Component	Microtubule organizing center	IEA
GO:0005815	Component	Microtubule organizing center	IMP	31630790
GO:0005815	Component	Microtubule organizing center	TAS	9566967
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005874	Component	Microtubule	IEA
GO:0005881	Component	Cytoplasmic microtubule	TAS	9566967
GO:0007020	Process	Microtubule nucleation	IBA
GO:0007020	Process	Microtubule nucleation	IEA
GO:0007020	Process	Microtubule nucleation	TAS	9566967
GO:0007420	Process	Brain development	IMP	31630790
GO:0016020	Component	Membrane	HDA	19946888
GO:0031122	Process	Cytoplasmic microtubule organization	IBA
GO:0036064	Component	Ciliary basal body	IDA
GO:0043015	Function	Gamma-tubulin binding	IBA
GO:0043015	Function	Gamma-tubulin binding	IEA
GO:0051011	Function	Microtubule minus-end binding	IBA
GO:0051225	Process	Spindle assembly	IBA
GO:0051321	Process	Meiotic cell cycle	IBA
GO:0065003	Process	Protein-containing complex assembly	TAS	9566967

Other IDs

• MIM: 617817
• HGNC: 18599
• e!Ensembl: ENSG00000130640

Protein

• UniProt ID: Q9BSJ2
• Protein name: Gamma-tubulin complex component 2 (GCP-2) (hGCP2) (Gamma-ring complex protein 103 kDa) (h103p) (hGrip103) (Spindle pole body protein Spc97 homolog) (hSpc97)
• Protein function: Component of the gamma-tubulin ring complex (gTuRC) which mediates microtubule nucleation (PubMed:38305685, PubMed:38609661, PubMed:39321809, PubMed:9566967). The gTuRC regulates the minus-end nucleation of alpha-beta tubulin heterodimers that g
• PDB: 6V6B, 6V6S, 6X0V, 7AS4, 7QJ0, 7QJ1, 7QJ2, 7QJ3, 7QJ4, 7QJ5, 7QJ6, 7QJ7, 7QJ8, 7QJ9, 7QJA, 7QJB, 7QJC, 7QJD, 8Q62, 8RX1, 8VRD, 8VRJ, 8VRK, 9H9P
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF17681	GCP_N_terminal	218 → 506	Gamma tubulin complex component N-terminal	Domain
  PF04130	GCP_C_terminal	509 → 865	Gamma tubulin complex component C-terminal	Domain

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitously expressed.
• Sequence:

  MSEFRIHHDVNELLSLLRVHGGDGAEVYIDLLQKNRTPYVTTTVSAHSAKVKIAEFSRTP
  EDFLKKYDELKSKNTRNLDPLVYLLSKLTEDKETLQYLQQNAKERAELAAAAVGSSTTSI
  NVPAAASKISMQELEELRKQLGSVATGSTLQQSLELKRKMLRDKQNKKNSGQHLPIFPAW
  VYERPALIGDFLIGAGISTDTALPIGTLPLASQESAVVEDLLYVLVGVDGRYVSAQPLAG
  RQSRTFLVDPNLDLSIRELVHRILPVAASYSAVTRFIEEKSSFEYGQVNHALAAAMRTLV
  KEHLILVSQLEQLHRQGLLSLQKLWFYIQPAMRTMDILASLATSVDKGECLGGSTLSLLH
  DRSFSYTGDSQAQELCLYLTKAASAPYFEVLEKWIYRGIIHDPYSEFMVEEHELRKERIQ
  EDYNDKYWDQRYTIVQQQIPSFLQKMADKILSTGKYLNVVRECGHDVTCPVAKEIIYTLK
  ERAYVEQIEKAFNYASKVLLDFLMEEKELVAHLRSIKRYFLMDQGDFFVHFMDLAEEELR
  KPVEDITPPRLEALLELALRMSTANTDPFKDDLKIDLMPHDLITQLLRVLAIETKQEKAM
  AHADPTELALSGLEAFSFDYIVKWPLSLIINRKALTRYQMLFRHMFYCKHVERQLCSVWI
  SNKTAKQHSLHSAQWFAGAFTLRQRMLNFVQNIQYYMMFEVMEPTWHILEKNLKSASNID
  DVLGHHTGFLDTCLKDCMLTNPELLKVFSKLMSVCVMFTNCMQKFTQSMKLDGELGGQTL
  EHSTVLGLPAGAEERARKELARKHLAEHADTVQLVSGFEATINKFDKNFSAHLLDLLARL
  SIYSTSDCEHGMASVISRLDFNGFYTERLERLSAERSQKATPQVPVLRGPPAPAPRVAVT
  AQ

• Sequence length: 902

Pathways

Reactome:

Recruitment of mitotic centrosome proteins and complexes
Recruitment of NuMA to mitotic centrosomes

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
Abnormality of neuronal migration	Pathogenic	rs1589822227	RCV001027406	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures	Pathogenic	rs2493637870, rs1589822227	RCV003388960 RCV000993672	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cervical cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 15	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LISSENCEPHALY SYNDROME, NORMAN-ROBERTS TYPE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALFORMATIONS OF CORTICAL DEVELOPMENT, GROUP II	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TUBGCP2-related disorder	Likely benign; Uncertain significance; Conflicting classifications of pathogenicity; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anencephaly	Anencephaly	BEFREE	20047525		★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	BEFREE	17197447		★☆☆☆☆ Found in Text Mining only
Astrocytoma	Astrocytoma	BEFREE	26079448		★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	BEFREE	19394322		★☆☆☆☆ Found in Text Mining only
Cutaneous Mastocytosis	Cutaneous mastocytosis	BEFREE	22886775		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	31630790	Associate	★☆☆☆☆ Found in Text Mining only
Elliptocytosis 1	Hereditary elliptocytosis	Pubtator	31630790	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	26079448		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	26079448		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	31630790		★☆☆☆☆ Found in Text Mining only
Guillain-Barre Syndrome	Guillain-Barre Syndrome	BEFREE	28147379		★☆☆☆☆ Found in Text Mining only
Guillain-Barre Syndrome, Familial	Guillain-Barre Syndrome	BEFREE	28147379		★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	BEFREE	31630790		★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	Pubtator	31630790	Associate	★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development Group II	Cortical development malformation	Pubtator	31630790	Associate	★☆☆☆☆ Found in Text Mining only
Meningomyelocele	Meningomyelocele	BEFREE	20047525		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	31630790		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	31630790	Associate	★☆☆☆☆ Found in Text Mining only
Myocardial Infarction	Myocardial Infarction	BEFREE	22886775		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	21236563, 26079448		★☆☆☆☆ Found in Text Mining only
Neural Tube Defects	Neural Tube Defect	BEFREE	20047525		★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	Pubtator	36672848	Associate	★☆☆☆☆ Found in Text Mining only