TBC1D8B

TBC1 domain family member 8B, the group of EF-hand domain containing|GRAM domain containing

Basic information

Region (hg38): X:106802673-106876150

Links

ENSG00000133138

∙ NCBI:54885 ∙ OMIM:301027 ∙ HGNC:24715 ∙ Uniprot:Q0IIM8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
nephrotic syndrome, type 20 (Limited), mode of inheritance: XL
nephrotic syndrome, type 20 (Strong), mode of inheritance: XL
nephrotic syndrome, type 20 (Moderate), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 20	XL	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	Renal	30661770
Renal transplant has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D8B gene.

not_provided (113 variants)
not_specified (108 variants)
TBC1D8B-related_disorder (27 variants)
Nephrotic_syndrome,_type_20 (22 variants)
Nephrotic_syndrome (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D8B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017752.3. 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			2 clinvar	16 clinvar	7 clinvar	25
missense	2 clinvar	2 clinvar	143 clinvar	16 clinvar	3 clinvar	166
nonsense	1 clinvar	1 clinvar	2 clinvar			4
start loss						0
frameshift		2 clinvar	2 clinvar	1 clinvar		5
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	3	5	150	33	10

Highest pathogenic variant AF is 0.000033980425

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D8B	protein_coding	protein_coding	ENST00000357242	21	73466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.95e-9	0.998	125646	27	70	125743	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0570	372	375	0.992	0.0000261	7389
Missense in Polyphen		125	128.99	0.96907		2410
Synonymous	0.838	118	130	0.907	0.00000867	2028
Loss of Function	2.83	20	39.1	0.511	0.00000291	755

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00118
Ashkenazi Jewish	0.000690	0.000496
East Asian	0.00234	0.00174
Finnish	0.00	0.00
European (Non-Finnish)	0.000291	0.000202
Middle Eastern	0.00234	0.00174
South Asian	0.000575	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).;
Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Intolerance Scores

loftool: 0.645
rvis_EVS: -1.15
rvis_percentile_EVS: 6.32

Haploinsufficiency Scores

pHI: 0.230
hipred: Y
hipred_score: 0.544
ghis: 0.541

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.244

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tbc1d8b
Phenotype

Gene ontology

Biological process: intracellular protein transport;activation of GTPase activity
Cellular component: cell
Molecular function: GTPase activator activity;calcium ion binding;Rab GTPase binding