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 1 (Supportive), mode of inheritance: AR
microcephaly and chorioretinopathy 3 (Strong), 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 (482 variants)
Inborn_genetic_diseases (65 variants)
not_specified (14 variants)
Microcephaly_and_chorioretinopathy_3 (11 variants)
TUBGCP4-related_disorder (7 variants)
Retinal_dystrophy (2 variants)
Optic_atrophy (2 variants)
Autosomal_recessive_chorioretinopathy-microcephaly_syndrome (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 TUBGCP4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014444.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar	1 clinvar	2 clinvar	121 clinvar	4 clinvar	129
missense		1 clinvar	157 clinvar	5 clinvar		163
nonsense	16 clinvar	3 clinvar	1 clinvar			20
start loss						0
frameshift	11 clinvar	3 clinvar	1 clinvar			15
splice donor/acceptor (+/-2bp)		7 clinvar				7
Total	28	15	161	126	4

Highest pathogenic variant AF is 0.000687146

Loading clinvar variants...

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
Phenotype

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