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

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Malignant tumor of urinary bladder	Likely pathogenic	rs753289059	RCV005913573
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
Microcephaly and chorioretinopathy with or without intellectual disability	Pathogenic	rs772174079, rs192919234	RCV000194400 RCV000193685
TUBGCP6-related disorder	Likely pathogenic	rs2519135002	RCV003404482

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Likely benign; Benign	rs55831939, rs149231425, rs34455105	RCV005912927 RCV005914287 RCV005922105
Adrenocortical carcinoma, hereditary	Benign	rs149231425, rs34455105	RCV005914291 RCV005922106
Cervical cancer	Uncertain significance; Benign	rs757545083, rs149231425	RCV005911160 RCV005914292
Cholangiocarcinoma	Benign	rs149231425	RCV005914300
Clear cell carcinoma of kidney	Benign; Likely benign	rs139343360	RCV005906117
Colorectal cancer	Benign	rs149231425, rs34455105	RCV005914294 RCV005922108
Gastric cancer	Benign; Likely benign; Uncertain significance	rs149231425, rs118091943, rs758447540, rs139343360	RCV005914296 RCV005921036 RCV005928389 RCV005906118
Hepatocellular carcinoma	Benign	rs149231425	RCV005914288
Intellectual disability	Uncertain significance	rs570025532	RCV005626676
Lung cancer	Benign	rs149231425	RCV005914301
Malignant lymphoma, large B-cell, diffuse	Benign	rs149231425, rs5771241, rs5771109	RCV005914293 RCV005915495 RCV005915663
Malignant tumor of esophagus	Benign	rs149231425	RCV005914289
Melanoma	Benign; Likely benign	rs149231425, rs139343360	RCV005914299 RCV005906120
Microcephaly	Uncertain significance	rs144692967	RCV001252885
Nonpapillary renal cell carcinoma	Benign	rs149231425	RCV005914290
Optic atrophy	Uncertain significance	rs745344235, rs750355124	RCV004815698 RCV004816353
Ovarian serous cystadenocarcinoma	Uncertain significance	rs765557133	RCV005910993
Retinal dystrophy	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	rs371357025, rs772567265, rs574080138, rs201277381, rs369896334, rs751077211, rs538912634, rs201406500, rs377471604, rs185642293, rs1297233801, rs1351314150, rs201914434	RCV004815469 RCV004816845 RCV004816855 RCV004816744 RCV004816971 RCV004817093 RCV004817118 RCV004813641 RCV004813567 RCV004813897 RCV004813949 RCV004815307 RCV004815285
Sarcoma	Benign; Likely benign	rs149231425, rs376828922, rs1030796393	RCV005914295 RCV005924276 RCV005921175
See cases	Uncertain significance	rs1205319610	RCV002252723
Thymoma	Benign	rs149231425	RCV005914298
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	rs139343360	RCV005906119
Uterine carcinosarcoma	Benign	rs149231425, rs5771241, rs34455105	RCV005914297 RCV005915496 RCV005922109
Uterine corpus endometrial carcinoma	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	rs757545083, rs776467377, rs149231425, rs113592725, rs34455105, rs114942206	RCV005911161 RCV005912830 RCV005914302 RCV005909780 RCV005922110 RCV005899907
Uveal melanoma	Benign	rs5771241, rs34455105	RCV005915494 RCV005922107

Associations from Text Mining
Disease Name	Relationship Type	References
Carcinoma Pancreatic Ductal	Associate	37196196
Chromosome Duplication	Associate	31874114
Cone Rod Dystrophies	Associate	31077665
Familial Exudative Vitreoretinopathies	Associate	33137195
Learning Disabilities	Associate	31077665
Microcephaly	Associate	33137195
Microcephaly with Chorioretinopathy Autosomal Dominant	Associate	33137195
Prodromal Symptoms	Associate	37196196
Retinal Diseases	Associate	31077665, 33137195
Sveinsson Chorioretinal Atrophy	Associate	33137195