TUBGCP4

tubulin gamma complex associated protein 4, the group of Tubulin gamma complex associated protein family

Basic information

Region (hg38): 15:43369221-43409771

Links

ENSG00000137822 ∙ NCBI:27229 ∙ OMIM:609610 ∙ HGNC:16691 ∙ Uniprot:Q9UGJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly and chorioretinopathy 3 (Strong), mode of inheritance: AR
• microcephaly and chorioretinopathy 1 (Supportive), mode of inheritance: AR
• microcephaly and chorioretinopathy 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly and chorioretinopathy, autosomal recessive 3	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	Craniofacial; Neurologic; Ophthalmologic	25817018

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TUBGCP4 gene.

• not provided (23 variants)
• Microcephaly and chorioretinopathy 3 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBGCP4 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				98	5	103
missense			140	5		145
nonsense	16	2	1			19
start loss						0
frameshift	7	3	1			11
inframe indel						0
splice donor/acceptor (+/-2bp)		7				7
splice region	1	1	17	16	1	36
non coding			8	128	33	169
Total	23	12	150	231	38

Highest pathogenic variant AF is 0.00000750

Variants in TUBGCP4

This is a list of pathogenic ClinVar variants found in the TUBGCP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43369686-A-G		ZSCAN29-related disorder	Likely benign (Apr 12, 2022)
15-43369765-T-C		not specified	Uncertain significance (Oct 06, 2022)
15-43369879-G-A		not specified	Uncertain significance (Jun 28, 2023)
15-43370961-G-C			Likely benign (Feb 07, 2019)
15-43370975-ACCCCGG-A			Benign (Jul 08, 2018)
15-43370975-A-ACCCCGG			Benign (Aug 27, 2019)
15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGGCCCCGG			Likely benign (Sep 26, 2019)
15-43370975-A-ACCCCGGCCCCGGCCCCGGCCCCGG			Likely benign (Jul 31, 2018)
15-43370975-A-ACCCCGGCCCCGG			Benign (Jul 17, 2018)
15-43371012-A-G			Likely benign (Mar 11, 2019)
15-43371363-C-T			Likely benign (Jan 13, 2024)
15-43371365-A-C			Uncertain significance (Aug 15, 2022)
15-43371371-T-C			Uncertain significance (Aug 09, 2022)
15-43371381-G-C			Likely benign (Jan 18, 2024)
15-43371382-A-G			Uncertain significance (Nov 08, 2022)
15-43371384-C-T			Likely benign (Aug 09, 2022)
15-43371385-G-A			Uncertain significance (Sep 06, 2022)
15-43371394-G-A		Inborn genetic diseases	Uncertain significance (May 31, 2023)
15-43371395-G-C			Uncertain significance (Sep 01, 2021)
15-43371405-C-T			Likely benign (Jul 14, 2021)
15-43371410-G-A			Pathogenic (Sep 08, 2022)
15-43371426-C-T			Likely benign (Oct 16, 2023)
15-43371445-G-T			Likely benign (Jul 14, 2022)
15-43376032-G-A			Likely benign (Aug 17, 2018)
15-43376078-C-T			Likely benign (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBGCP4	protein_coding	protein_coding	ENST00000564079	18	37875

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.70e-9	0.999	124713	0	85	124798	0.000341

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	227	366	0.620	0.0000201	4361
Missense in Polyphen		32	65.869	0.48581		845
Synonymous	0.423	134	140	0.955	0.00000704	1306
Loss of Function	3.03	21	42.2	0.497	0.00000232	443

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000327
Ashkenazi Jewish	0.00278	0.00278
East Asian	0.000445	0.000445
Finnish	0.000325	0.000325
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000445	0.000445
South Asian	0.000363	0.000360
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Gamma-tubulin complex is necessary for microtubule nucleation at the centrosome.
• 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)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.710
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.0762
• hipred: Y
• hipred_score: 0.706
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.717

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tubgcp4

Zebrafish Information Network

• Gene name: tubgcp4
• Affected structure: retinal rod cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

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