TBC1D1

TBC1 domain family member 1

Basic information

Region (hg38): 4:37891084-38139175

Links

ENSG00000065882

∙ NCBI:23216 ∙ OMIM:609850 ∙ HGNC:11578 ∙ Uniprot:Q86TI0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital anomaly of kidney and urinary tract (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D1 gene.

Inborn_genetic_diseases (163 variants)
TBC1D1-related_disorder (45 variants)
not_specified (36 variants)
not_provided (20 variants)
Congenital_anomaly_of_kidney_and_urinary_tract (1 variants)
Non-syndromic_renal_or_urinary_tract_malformation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001396959.1. 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				22 clinvar	3 clinvar	25
missense			159 clinvar	24 clinvar	1 clinvar	184
nonsense						0
start loss						0
frameshift			3 clinvar	1 clinvar		4
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	163	47	4

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D1	protein_coding	protein_coding	ENST00000261439	19	248089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-13	1.00	125641	1	106	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	623	678	0.918	0.0000411	7685
Missense in Polyphen		205	240.33	0.853		2691
Synonymous	-0.0361	279	278	1.00	0.0000189	2229
Loss of Function	3.46	31	59.9	0.518	0.00000352	634

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000772	0.000707
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000437	0.000431
Middle Eastern	0.000772	0.000707
South Asian	0.000239	0.000196
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s). May play a role in the cell cycle and differentiation of various tissues. Involved in the trafficking and translocation of GLUT4-containing vesicles and insulin-stimulated glucose uptake into cells (By similarity). {ECO:0000250}.;
Pathway: AMPK signaling pathway - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Vesicle-mediated transport;Membrane Trafficking;Translocation of GLUT4 to the plasma membrane (Consensus)

Recessive Scores

pRec: 0.206

Intolerance Scores

loftool: 0.881
rvis_EVS: 0.01
rvis_percentile_EVS: 54.16

Haploinsufficiency Scores

pHI: 0.163
hipred: Y
hipred_score: 0.554
ghis: 0.456

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.615

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tbc1d1
Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); normal phenotype;

Gene ontology

Biological process: intracellular protein transport;regulation of protein localization;membrane organization;activation of GTPase activity;regulation of cilium assembly
Cellular component: nucleus;cytosol
Molecular function: GTPase activator activity;protein binding;Rab GTPase binding