TUBGCP6

tubulin gamma complex associated protein 6, the group of Tubulin gamma complex associated protein family

Basic information

Region (hg38): 22:50217688-50245023

Links

ENSG00000128159 ∙ NCBI:85378 ∙ OMIM:610053 ∙ HGNC:18127 ∙ Uniprot:Q96RT7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly and chorioretinopathy 1 (Definitive), mode of inheritance: AR
• microcephaly and chorioretinopathy 1 (Supportive), mode of inheritance: AR
• microcephaly and chorioretinopathy 1 (Strong), mode of inheritance: AR
• microcephaly and chorioretinopathy 1 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly and chorioretinopathy, autosomal recessive 1	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	5936364; 22279524; 25344692

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TUBGCP6 gene.

• not provided (1787 variants)
• Inborn genetic diseases (132 variants)
• not specified (72 variants)
• Microcephaly and chorioretinopathy 1 (62 variants)
• TUBGCP6-related condition (2 variants)
• Microcephaly and chorioretinopathy with or without intellectual disability (2 variants)
• Microcephaly (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBGCP6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous		1	13	437	18	469
missense			834	61	21	916
nonsense	21	4	4	3		32
start loss				1		1
frameshift	37	6	6	1		50
inframe indel		1	26			27
splice donor/acceptor (+/-2bp)	1	17				18
splice region			27	46	4	77
non coding			6	183	31	220
Total	59	29	889	686	70

Highest pathogenic variant AF is 0.0000592

Variants in TUBGCP6

This is a list of pathogenic ClinVar variants found in the TUBGCP6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-50217697-G-A			Likely benign (Jun 19, 2019)
22-50217738-A-C		Microcephaly and chorioretinopathy 1	Pathogenic (Jan 01, 2012)
22-50217740-G-A			Uncertain significance (May 19, 2022)
22-50217742-G-A			Likely benign (Dec 09, 2023)
22-50217743-T-C			Uncertain significance (Jan 22, 2020)
22-50217745-C-T			Likely benign (Dec 12, 2023)
22-50217750-A-G			Uncertain significance (Aug 23, 2021)
22-50217752-T-G			Uncertain significance (Dec 13, 2022)
22-50217753-A-AGTT			Uncertain significance (Aug 08, 2022)
22-50217756-T-A			Uncertain significance (Sep 02, 2021)
22-50217760-G-A			Likely benign (Apr 26, 2023)
22-50217760-G-GC			Uncertain significance (Feb 03, 2022)
22-50217761-A-T			Uncertain significance (Oct 19, 2020)
22-50217763-G-A			Likely benign (Feb 21, 2023)
22-50217765-T-A		See cases	Uncertain significance (Oct 25, 2022)
22-50217769-G-A			Likely benign (Aug 23, 2022)
22-50217770-C-T			Uncertain significance (Sep 13, 2022)
22-50217771-G-A			Uncertain significance (Mar 30, 2022)
22-50217772-C-T			Likely benign (Mar 04, 2022)
22-50217777-G-A			Likely benign (Oct 05, 2023)
22-50217778-A-G			Likely benign (Sep 25, 2020)
22-50217780-A-G			Uncertain significance (May 13, 2021)
22-50217792-G-A			Uncertain significance (Aug 16, 2022)
22-50217794-G-A		Inborn genetic diseases	Uncertain significance (May 23, 2023)
22-50217795-G-C			Uncertain significance (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBGCP6	protein_coding	protein_coding	ENST00000248846	25	27304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.56e-31	0.112	125455	0	293	125748	0.00117

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.944	1215	1.13e+3	1.08	0.0000745	11690
Missense in Polyphen		438	417.76	1.0484		4608
Synonymous	-4.14	619	501	1.24	0.0000370	3765
Loss of Function	2.10	59	79.2	0.745	0.00000407	847

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00203	0.00201
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.00104	0.00103
Finnish	0.00201	0.00199
European (Non-Finnish)	0.00126	0.00123
Middle Eastern	0.00104	0.00103
South Asian	0.00110	0.00108
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Gamma-tubulin complex is necessary for microtubule nucleation at the centrosome. {ECO:0000269|PubMed:11694571}.
• Disease: DISEASE: Microcephaly and chorioretinopathy, autosomal recessive, 1 (MCCRP1) [MIM:251270]: A syndrome characterized by microcephaly, cognitive impairment, underdeveloped retina and choroid, and epilepsy in some patients. The more anterior parts of the retina, near the periphery and pars plana, have a grayish hue and diminutive vasculature similar to retinopathy of prematurity. Visual impairment becomes evident during the first year of life. {ECO:0000269|PubMed:22279524}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Recruitment of mitotic centrosome proteins and complexes;Centrosome maturation;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Intolerance Scores

• loftool: 0.892
• rvis_EVS: -2.6
• rvis_percentile_EVS: 0.82

Haploinsufficiency Scores

• pHI: 0.0890
• hipred: N
• hipred_score: 0.443
• ghis: 0.596

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tubgcp6

Gene ontology

• Biological process: mitotic cell cycle;microtubule nucleation;cytoplasmic microtubule organization;spindle assembly;meiotic cell cycle;microtubule nucleation by interphase microtubule organizing center
• Cellular component: spindle pole;equatorial microtubule organizing center;gamma-tubulin complex;centrosome;cytosol;microtubule;gamma-tubulin ring complex;gamma-tubulin small complex;membrane
• Molecular function: microtubule binding;gamma-tubulin binding;microtubule minus-end binding