TBC1D16

TBC1 domain family member 16

Basic information

Region (hg38): 17:79932342-80035872

Links

ENSG00000167291 ∙ NCBI:125058 ∙ OMIM:616637 ∙ HGNC:28356 ∙ Uniprot:Q8TBP0 ∙ 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 TBC1D16 gene.

• Inborn genetic diseases (48 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D16 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				1	3	4
missense			48			48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	1	3

Variants in TBC1D16

This is a list of pathogenic ClinVar variants found in the TBC1D16 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-79940873-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-79940887-G-A		not specified	Uncertain significance (Mar 06, 2023)
17-79940936-T-C		not specified	Uncertain significance (Feb 06, 2023)
17-79940951-C-T		not specified	Uncertain significance (Feb 22, 2023)
17-79940972-C-T		not specified	Uncertain significance (Aug 15, 2023)
17-79940983-C-T		not specified	Uncertain significance (Jan 24, 2024)
17-79940998-G-T		not specified	Uncertain significance (Dec 01, 2022)
17-79941050-C-T		not specified	Uncertain significance (Jul 20, 2021)
17-79941066-G-C		not specified	Uncertain significance (Feb 27, 2023)
17-79941070-C-T		not specified	Uncertain significance (Jan 10, 2023)
17-79942064-C-T		not specified	Uncertain significance (May 26, 2022)
17-79942065-G-A		not specified	Uncertain significance (Dec 21, 2022)
17-79942077-C-G		not specified	Uncertain significance (Aug 12, 2022)
17-79942080-C-T		not specified	Uncertain significance (Aug 21, 2023)
17-79942104-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-79942127-G-A		not specified	Uncertain significance (Nov 02, 2023)
17-79942150-G-A			Likely benign (Jul 01, 2022)
17-79942171-G-A			Benign (Oct 19, 2017)
17-79942205-G-A		not specified	Uncertain significance (Jun 06, 2023)
17-79944958-G-A		not specified	Uncertain significance (Oct 27, 2021)
17-79944991-G-A		not specified	Uncertain significance (Jan 09, 2024)
17-79945004-C-A		not specified	Uncertain significance (Mar 21, 2023)
17-79945011-A-G		not specified	Uncertain significance (Aug 10, 2021)
17-79945059-G-A		not specified	Uncertain significance (Nov 21, 2022)
17-79945075-C-T		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D16	protein_coding	protein_coding	ENST00000310924	11	103506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.57e-7	0.996	125698	0	48	125746	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.559	467	502	0.930	0.0000356	4929
Missense in Polyphen		149	195.11	0.76369		1951
Synonymous	0.00361	233	233	1.00	0.0000185	1542
Loss of Function	2.56	16	31.5	0.507	0.00000149	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000394	0.000388
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000196	0.000185
European (Non-Finnish)	0.000228	0.000211
Middle Eastern	0.0000544	0.0000544
South Asian	0.000265	0.000261
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.684
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.73

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.492
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.233

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d16

Gene ontology

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