TBC1D10B

TBC1 domain family member 10B

Basic information

Region (hg38): 16:30357102-30370494

Links

ENSG00000169221 ∙ NCBI:26000 ∙ OMIM:613620 ∙ HGNC:24510 ∙ Uniprot:Q4KMP7 ∙ 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 TBC1D10B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D10B 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						0
missense			59	1		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	1	0

Variants in TBC1D10B

This is a list of pathogenic ClinVar variants found in the TBC1D10B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30357963-C-T		not specified	Uncertain significance (Jun 12, 2023)
16-30358009-G-A		not specified	Uncertain significance (Jan 11, 2023)
16-30358014-T-C		not specified	Uncertain significance (Feb 22, 2023)
16-30358015-C-T		not specified	Uncertain significance (Feb 06, 2024)
16-30358029-A-G		not specified	Uncertain significance (May 15, 2023)
16-30358032-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-30358041-C-T		not specified	Uncertain significance (Feb 10, 2022)
16-30358087-T-C		not specified	Uncertain significance (Jun 12, 2023)
16-30358088-C-G		not specified	Uncertain significance (Dec 15, 2023)
16-30358146-C-A		not specified	Uncertain significance (Jul 29, 2023)
16-30358146-C-T		not specified	Likely benign (Jul 06, 2021)
16-30358147-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-30358155-T-C		not specified	Uncertain significance (Apr 23, 2024)
16-30358156-C-T		not specified	Uncertain significance (May 11, 2022)
16-30358168-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-30358189-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-30358206-C-T		not specified	Uncertain significance (May 21, 2024)
16-30358207-G-A		not specified	Uncertain significance (Feb 17, 2024)
16-30358324-C-T		not specified	Uncertain significance (Oct 21, 2021)
16-30358327-G-T		not specified	Uncertain significance (Feb 21, 2024)
16-30358330-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-30358354-C-A		not specified	Uncertain significance (Feb 28, 2023)
16-30358429-G-A		not specified	Uncertain significance (Apr 04, 2023)
16-30358432-G-A		not specified	Uncertain significance (Jul 10, 2023)
16-30358434-C-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D10B	protein_coding	protein_coding	ENST00000409939	9	13163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000783	122214	0	2	122216	0.00000818

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	288	397	0.725	0.0000256	4958
Missense in Polyphen		43	86.935	0.49462		938
Synonymous	0.858	148	162	0.914	0.00000930	1799
Loss of Function	4.69	2	29.5	0.0678	0.00000162	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000110	0.000101
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000928	0.00000906
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as GTPase-activating protein for RAB3A, RAB22A, RAB27A, AND RAB35. Does not act on RAB2A and RAB6A. {ECO:0000269|PubMed:16923811, ECO:0000269|PubMed:19077034}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.372
• hipred: Y
• hipred_score: 0.572
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d10b

Gene ontology

• Biological process: intracellular protein transport;retrograde transport, endosome to Golgi;regulation of GTPase activity;activation of GTPase activity;regulation of cilium assembly
• Cellular component: cytosol;plasma membrane
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding