TBC1D8

TBC1 domain family member 8, the group of GRAM domain containing

Basic information

Region (hg38): 2:101007227-101252866

Links

ENSG00000204634 ∙ NCBI:11138 ∙ ∙ HGNC:17791 ∙ Uniprot:O95759 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D8 gene.

• Inborn genetic diseases (53 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D8 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					3	3
missense			50	3	1	54
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		3	4
Total	0	0	51	3	8

Variants in TBC1D8

This is a list of pathogenic ClinVar variants found in the TBC1D8 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-101007861-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-101007866-T-G		not specified	Uncertain significance (Aug 23, 2021)
2-101007870-A-AAAG			Benign (Jul 15, 2020)
2-101007916-A-G		not specified	Uncertain significance (May 31, 2023)
2-101008047-G-C		not specified	Uncertain significance (Jul 06, 2021)
2-101008064-A-G			Benign (Jan 01, 2024)
2-101008099-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-101008134-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-101008185-A-G		not specified	Uncertain significance (Jan 29, 2024)
2-101010966-T-C		not specified	Uncertain significance (Oct 10, 2023)
2-101011453-T-C		not specified	Uncertain significance (May 09, 2022)
2-101011456-G-T		not specified	Uncertain significance (Apr 12, 2022)
2-101011463-C-T			Benign (Jan 11, 2019)
2-101011489-A-G		not specified	Uncertain significance (Aug 26, 2022)
2-101018825-C-T			Benign (May 24, 2021)
2-101018907-G-A			Benign (May 17, 2021)
2-101018985-ATTTCTGTGCTAG-A			Uncertain significance (Dec 15, 2023)
2-101019007-TA-T			Uncertain significance (Oct 09, 2022)
2-101019076-C-T			Benign (May 14, 2021)
2-101021737-T-C		not specified	Uncertain significance (Feb 12, 2024)
2-101022316-T-G		not specified	Uncertain significance (Jan 26, 2022)
2-101022346-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-101022377-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-101022430-A-G		not specified	Uncertain significance (May 15, 2023)
2-101022431-T-C		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D8	protein_coding	protein_coding	ENST00000376840	20	245250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.60e-13	1.00	125210	0	97	125307	0.000387

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	553	653	0.847	0.0000392	7531
Missense in Polyphen		191	259.44	0.73619		2926
Synonymous	0.186	281	285	0.986	0.0000196	2155
Loss of Function	3.44	30	58.4	0.514	0.00000349	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000972	0.000928
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000277	0.000272
Finnish	0.000329	0.000324
European (Non-Finnish)	0.000443	0.000432
Middle Eastern	0.000277	0.000272
South Asian	0.000229	0.000229
Other	0.000674	0.000655

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).
• Pathway: Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.21

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.510
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d8

Gene ontology

• Biological process: intracellular protein transport;blood circulation;positive regulation of cell population proliferation;activation of GTPase activity;regulation of cilium assembly
• Cellular component: cell;membrane
• Molecular function: GTPase activator activity;Rab GTPase binding