TUBGCP6 (tubulin gamma complex component 6)

Gene

• Entrez ID: 85378
• Gene name: Tubulin gamma complex component 6
• Gene symbol: TUBGCP6
• Synonyms (NCBI Gene): GCP-6, GCP6, MCCRP, MCCRP1, MCPHCR
• Chromosome: 22
• Chromosome location: 22q13.33
• Summary: The protein encoded by this gene is part of a large multisubunit complex required for microtubule nucleation at the centrosome. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs148626062	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs192919234	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs368449236	T>C	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, missense variant
rs724159975	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs724159976	C>A,T	Pathogenic	Non coding transcript variant, intron variant, coding sequence variant, stop gained, missense variant
rs724159997	G>A	Pathogenic	Intron variant, missense variant, coding sequence variant, non coding transcript variant
rs727502807	->A	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs760024638	->G	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant, non coding transcript variant
rs762453492	TGGCGGAGGGCAGA>-	Likely-pathogenic	Splice acceptor variant, intron variant
rs770971683	C>A	Likely-pathogenic	Splice donor variant
rs772174079	G>A,T	Pathogenic	Synonymous variant, non coding transcript variant, coding sequence variant, stop gained
rs886041788	C>T	Pathogenic	Splice donor variant
rs1260456579	G>A	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1427049971	C>-,CC	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1444741505	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1555907238	->CCCTCCCCGCAGCCC	Likely-pathogenic	Non coding transcript variant, inframe insertion, intron variant, coding sequence variant
rs1555907270	G>A	Likely-pathogenic	Non coding transcript variant, intron variant, coding sequence variant, stop gained
rs1555908577	G>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1602510452	C>T	Likely-pathogenic	Non coding transcript variant, intron variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016913	hsa-miR-335-5p	Microarray	18185580
MIRT043114	hsa-miR-324-5p	CLASH	23622248
MIRT041292	hsa-miR-193b-3p	CLASH	23622248

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:0000931	Component	Gamma-tubulin ring complex	IDA	11694571
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	21399614
GO:0005813	Component	Centrosome	IEA
GO:0005815	Component	Microtubule organizing center	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005874	Component	Microtubule	IEA
GO:0007020	Process	Microtubule nucleation	IBA
GO:0007020	Process	Microtubule nucleation	IDA	11694571
GO:0007020	Process	Microtubule nucleation	IEA
GO:0008017	Function	Microtubule binding	IDA	11694571
GO:0016020	Component	Membrane	HDA	19946888
GO:0031122	Process	Cytoplasmic microtubule organization	IBA
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

Other IDs

• MIM: 610053
• HGNC: 18127
• e!Ensembl: ENSG00000128159

Protein

• UniProt ID: Q96RT7
• Protein name: Gamma-tubulin complex component 6 (GCP-6)
• Protein function: Component of the gamma-tubulin ring complex (gTuRC) which mediates microtubule nucleation (PubMed:11694571, PubMed:38305685, PubMed:38609661, PubMed:39321809). The gTuRC regulates the minus-end nucleation of alpha-beta tubulin heterodimers that
• PDB: 6M33, 6V6C, 6V6S, 6X0U, 7AS4, 7QJ0, 7QJ1, 7QJ2, 7QJ3, 7QJ4, 7QJ5, 7QJ6, 7QJ7, 7QJ8, 7QJ9, 7QJA, 7QJB, 7QJC, 7QJD, 7QJE, 8Q62, 8RX1, 8VRD, 8VRJ, 8VRK, 9H9P
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF17681	GCP_N_terminal	353 → 693	Gamma tubulin complex component N-terminal	Domain
  PF04130	GCP_C_terminal	1513 → 1816	Gamma tubulin complex component C-terminal	Domain

• Sequence:

  MASITQLFDDLCEALLPAAKTHLGQRSVNRKRAKRSLKKVAYNALFTNLFQDETQQLQPD
  MSKLPARNKILMLSFDLRVGGLGPKADRLEELVEELEAAPCCPLLEVGSVLDLLVQLAGS
  GPPQVLPRKRDYFLNNKHVGRNVPYSGYDCDDLSVFEMDVQSLISREECLCHSMIQETLQ
  VMEAAPGTGLPTVGLFSFGDPCGDRFERDTRVSLFGALVHSRTYDMDVRLGLPPVPDNAD
  LSGLAIKVPPSVDQWEDEGFQSASNLTPDSQSEPSVTPDVDLWEAALTYEASKRRCWERV
  GCPPGHREEPYLTEAGRDAFDKFCRLHQGELQLLAGGVLQAPQPVLVKECELVKDVLNVL
  IGVVSATFSLCQPAQAFVVKRGVHVSGASPESISSLLSEVAEYGTCYTRLSHFSLQPVLD
  SLYSKGLVFQAFTSGLRRYLQYYRACVLSTPPTLSLLTIGFLFKKLGRQLRYLAELCGVG
  AVLPGTCGGGPRAAFPTGVKLLSYLYQEALHNCSNEHYPVLLSLLKTSCEPYTRFIHDWV
  YSGVFRDAYGEFMIQVNHEYLSFRDKLYWTHGYVLISKEVEDCVPVFLKHIAHDIYVCGK
  TINLLKLCCPRHYLCWSDVPVPRISVIFSLEELKEIEKDCAVYVGRMERVARHSSVSKEE
  KELRMEIAKQELIAHAREAASRVLSALSDRQMSERMALDARKREQFQRLKEQFVKDQERR
  QAARQEELDDDFSYARELRDRERRLKSLEEELERKARQALVDHYSKLSAEAARREQKALW
  RIQRHRLESARLRFLLEDEKHIQEMLKAVSEAHQPQEPPDVLLSVHPQVTSPGPEHPEGG
  QGCDSGSAEQHSPAWDGWNRPGLLTPQPLKPLAVGAGGRGLQQAEGARPFSDSLSIGDFL
  PVGPGAEPSVQTGMVPLLEVALQTINLDLPPSAPGEAPAAASTQPSRPQEYDFSTVLRPA
  VATSPAPGPLQAAECSLGSSGLQLWEDSCGKMDACGSASRETLLPSHPPRRAALEEGSSQ
  PTERLFGQVSGGGLPTGDYASEIAPTRPRWNTHGHVSDASIRVGENVSDVAPTQPRWNTH
  GHVSNASISLGESVSDVAPTRPRWNIHGHVSNASIRVGENVSDVAPTRPRWNTHGHVSNA
  SIRVGENVSDVAPTRPRWNTHGHVSDASISLGESVSDMAPARPRWNTHGHVSDASISLGE
  SVSDMAPTRPRWNTHGHVSDTSIRVGENVSDVAPIRSRCNTHGHVSDASISLGEPVSDVV
  STRPRWNTHVPIPPPHMVLGALSPEAEPNTPRPQQSPPGHTSQSALSLGAQSTVLDCGPR
  LPVEVGPSLSSPSSGCGEGSISVGENVSDVAPTQPWWPNTPGDSVSEELGPGRSGDTEDL
  SPNWPLNSQEDTAAQSSPGRGEEAEASAAEAQGGEQAYLAGLAGQYHLERYPDSYESMSE
  PPIAHLLRPVLPRAFAFPVDPQVQSAADETAVQLSELLTLPVLMKRSITAPLAAHISLVN
  KAAVDYFFVELHLEAHYEALRHFLLMEDGEFAQSLSDLLFEKLGAGQTPGELLNPLVLNS
  VLSKALQCSLHGDTPHASNLSLALKYLPEVFAPNAPDVLSCLELRYKVDWPLNIVITEGC
  VSKYSGVFSFLLQLKLMMWALKDVCFHLKRTALLSHMAGSVQFRQLQLFKHEMQHFVKVI
  QGYIANQILHVTWCEFRARLATVGDLEEIQRAHAEYLHKAVFRGLLTEKAAPVMNVIHSI
  FSLVLKFRSQLISQAWGPPGGPRGAEHPNFALMQQSYNTFKYYSHFLFKVVTKLVNRGYQ
  PHLEDFLLRINFNNYYQDA

• Sequence length: 1819

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
Malignant tumor of urinary bladder	Likely pathogenic	rs753289059	RCV005913573	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Microcephaly and chorioretinopathy 1	Likely pathogenic; Pathogenic	rs951221380, rs776065095, rs2147184688, rs1056686381, rs752869602, rs727502807, rs724159975, rs724159976, rs724159997, rs192919234, rs1460482736, rs756544270, rs2519133759, rs760024638, rs387907019, rs1602510452, rs1444741505, rs2519122368, rs1444906763, rs770253928, rs2064470709	RCV005630946 RCV001783994 RCV005361868 RCV005628332 RCV005256834 RCV000149797 RCV000149798 RCV000149800 RCV000149801 RCV002298518 RCV003232911 RCV003389295 RCV003480012 RCV005256605 RCV000023794 RCV001007659 RCV001007658 RCV001255744 RCV001255849 RCV001255761 RCV001283844	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Microcephaly and chorioretinopathy with or without intellectual disability	Pathogenic	rs772174079, rs192919234	RCV000194400 RCV000193685	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
TUBGCP6-related disorder	Likely pathogenic	rs2519135002	RCV003404482	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTHMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CHORIORETINOPATHY AND MICROCEPHALY SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CHORIORETINOPATHY-MICROCEPHALY SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Intellectual disability	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY AND CHORIORETINOPATHY, AUTOSOMAL RECESSIVE, 1	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY WITH CHORIORETINOPATHY, AUTOSOMAL RECESSIVE	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinal dystrophy	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autosomal recessive chorioretinopathy-microcephaly syndrome	Chorioretinopathy-Microcephaly Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	37196196	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral cortical atrophy	Cerebral cortical atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Learning Disabilities	Learning disorders	Pubtator	31077665	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	30543990		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	Pubtator	33137195	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY AND CHORIORETINOPATHY, AUTOSOMAL RECESSIVE, 1	Microcephaly with Chorioretinopathy	GENOMICS_ENGLAND_DG	22279524		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY AND CHORIORETINOPATHY, AUTOSOMAL RECESSIVE, 1	Microcephaly with Chorioretinopathy	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly with Chorioretinopathy, Autosomal Recessive	Microcephaly with Chorioretinopathy	ORPHANET_DG	22279524		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly with Chorioretinopathy, Autosomal Recessive	Microcephaly with Chorioretinopathy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Primary microcephaly	Microcephaly	GENOMICS_ENGLAND_DG	22279524		★☆☆☆☆ Found in Text Mining only
Retinal Detachment	Retinal Detachment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal Diseases	BEFREE	25344692		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	31077665, 33137195	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Seckel syndrome	Seckel Syndrome	BEFREE	25344692		★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sveinsson Chorioretinal Atrophy	Sveinsson chorioretinal atrophy	Pubtator	33137195	Associate	★☆☆☆☆ Found in Text Mining only