TBC1D2

TBC1 domain family member 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 9:98199010-98255649

Links

ENSG00000095383 ∙ NCBI:55357 ∙ OMIM:609871 ∙ HGNC:18026 ∙ Uniprot:Q9BYX2 ∙ 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 TBC1D2 gene.

• Inborn genetic diseases (47 variants)
• not provided (11 variants)
• Mycotic Aneurysm, Intracranial (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D2 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					4	4
missense			44	6	5	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	6	9

Variants in TBC1D2

This is a list of pathogenic ClinVar variants found in the TBC1D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-98199422-C-T			Benign (Jun 14, 2018)
9-98199433-C-T		not specified	Uncertain significance (Dec 27, 2023)
9-98199436-C-T		not specified	Uncertain significance (Oct 20, 2023)
9-98199440-G-A			Likely benign (May 30, 2018)
9-98199448-C-T		not specified	Uncertain significance (Dec 16, 2023)
9-98199463-T-C		not specified	Uncertain significance (Jan 18, 2022)
9-98199487-C-T			Benign (May 18, 2018)
9-98199511-C-T		not specified	Uncertain significance (Sep 28, 2022)
9-98199547-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-98200284-G-A			Likely benign (Jun 18, 2018)
9-98201496-G-A			Benign (Apr 03, 2018)
9-98201574-C-T		not specified	Likely benign (Nov 05, 2021)
9-98201589-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-98201609-G-T		not specified	Uncertain significance (Dec 21, 2022)
9-98203298-G-A		not specified	Uncertain significance (Apr 22, 2022)
9-98203298-G-T		Mycotic Aneurysm, Intracranial	Uncertain significance (Oct 08, 2021)
9-98203353-G-C		not specified	Uncertain significance (Jul 14, 2023)
9-98203380-C-G		not specified	Uncertain significance (May 17, 2023)
9-98203403-G-A		not specified	Uncertain significance (Feb 15, 2023)
9-98208713-A-T		not specified	Uncertain significance (Aug 08, 2022)
9-98208716-G-A		not specified	Uncertain significance (Oct 04, 2022)
9-98208726-C-G		not specified	Uncertain significance (Nov 09, 2023)
9-98208762-A-C		not specified	Uncertain significance (Feb 17, 2022)
9-98208902-A-C		not specified	Uncertain significance (Jan 10, 2022)
9-98208920-C-T		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D2	protein_coding	protein_coding	ENST00000375066	13	56605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.99e-10	0.995	125588	1	159	125748	0.000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	484	554	0.874	0.0000352	5911
Missense in Polyphen		143	189.91	0.75298		2155
Synonymous	1.84	204	240	0.849	0.0000149	1862
Loss of Function	2.63	22	39.9	0.551	0.00000190	440

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.000997
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00234	0.00234
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000379	0.000308
Middle Eastern	0.00234	0.00234
South Asian	0.00187	0.00180
Other	0.000526	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as GTPase-activating protein for RAB7A. Signal effector acting as a linker between RAC1 and RAB7A, leading to RAB7A inactivation and subsequent inhibition of cadherin degradation and reduced cell-cell adhesion. {ECO:0000269|PubMed:20116244}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.886
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.58

Haploinsufficiency Scores

• pHI: 0.0863
• hipred: N
• hipred_score: 0.343
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.807

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: intracellular protein transport;positive regulation of GTPase activity;activation of GTPase activity;regulation of cilium assembly
• Cellular component: nucleus;cytosol;cell junction;cytoplasmic vesicle
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding;cadherin binding