TBC1D2B

TBC1 domain family member 2B

Basic information

Region (hg38): 15:77984036-78077724

Links

ENSG00000167202 ∙ NCBI:23102 ∙ OMIM:619152 ∙ HGNC:29183 ∙ Uniprot:Q9UPU7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with seizures and gingival overgrowth (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with seizures and gingival overgrowth	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; Dental; Musculoskeletal; Neurologic; Ophthalmologic	32623794

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D2B 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				7		7
missense			62	4	1	67
nonsense		3	2			5
start loss						0
frameshift		1				1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	4	64	12	1

Variants in TBC1D2B

This is a list of pathogenic ClinVar variants found in the TBC1D2B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-77998221-C-T		Inborn genetic diseases	Uncertain significance (Jan 31, 2024)
15-77998288-C-T			Likely benign (Sep 01, 2024)
15-77998291-G-T		Inborn genetic diseases	Uncertain significance (Feb 03, 2023)
15-77998300-G-A		Neurodevelopmental disorder with seizures and gingival overgrowth	Uncertain significance (May 25, 2022)
15-78001673-G-A			Uncertain significance (Dec 01, 2022)
15-78001706-T-C		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
15-78003358-C-T		Inborn genetic diseases	Uncertain significance (Apr 12, 2024)
15-78003382-G-A			Uncertain significance (Jul 01, 2024)
15-78003406-T-G		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
15-78003408-T-C		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
15-78003423-T-C			Likely benign (May 01, 2023)
15-78003481-G-A		Inborn genetic diseases	Uncertain significance (Dec 17, 2023)
15-78009007-A-T		Neurodevelopmental disorder with seizures and gingival overgrowth	Pathogenic (May 19, 2021)
15-78009031-C-T		Inborn genetic diseases	Uncertain significance (Dec 06, 2021)
15-78009032-G-A		TBC1D2B-related disorder	Likely pathogenic (May 29, 2024)
15-78009043-A-G		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
15-78009090-G-C		Neurodevelopmental disorder with seizures and gingival overgrowth	Pathogenic (May 19, 2021)
15-78009096-G-A			Likely benign (Jun 01, 2022)
15-78009109-A-G		Inborn genetic diseases	Uncertain significance (May 10, 2023)
15-78012819-C-T			Benign (Feb 01, 2024)
15-78012859-C-T		Inborn genetic diseases	Uncertain significance (Mar 20, 2024)
15-78012920-A-T		Inborn genetic diseases	Uncertain significance (Mar 27, 2023)
15-78013041-C-T			Likely benign (Apr 01, 2022)
15-78013047-C-A		Inborn genetic diseases	Uncertain significance (Jul 14, 2021)
15-78013060-C-T		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D2B	protein_coding	protein_coding	ENST00000300584	13	93689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-8	1.00	125554	0	39	125593	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	388	503	0.772	0.0000283	6268
Missense in Polyphen		120	197.99	0.60609		2324
Synonymous	-0.174	205	202	1.02	0.0000117	1861
Loss of Function	3.09	20	41.5	0.482	0.00000208	523

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000270
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000112	0.000109
Finnish	0.0000928	0.0000925
European (Non-Finnish)	0.000166	0.000159
Middle Eastern	0.000112	0.000109
South Asian	0.000163	0.000163
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein. {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.972
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.04

Haploinsufficiency Scores

• pHI: 0.177
• hipred: Y
• hipred_score: 0.554
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d2b
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype

Gene ontology

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