TBC1D17

TBC1 domain family member 17, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 19:49877666-49888750

Links

ENSG00000104946 ∙ NCBI:79735 ∙ OMIM:616659 ∙ HGNC:25699 ∙ Uniprot:Q9HA65 ∙ 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 TBC1D17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D17 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			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	0

Variants in TBC1D17

This is a list of pathogenic ClinVar variants found in the TBC1D17 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49878149-T-G		not specified	Uncertain significance (Jan 16, 2024)
19-49878195-A-T		not specified	Uncertain significance (Apr 26, 2024)
19-49878504-G-A		not specified	Uncertain significance (Nov 17, 2023)
19-49878537-G-A		not specified	Uncertain significance (May 30, 2024)
19-49878558-C-A		not specified	Uncertain significance (Apr 08, 2024)
19-49880288-G-C		not specified	Uncertain significance (Feb 28, 2024)
19-49880289-G-T		not specified	Uncertain significance (Jul 27, 2022)
19-49880370-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-49881275-G-T		not specified	Uncertain significance (Feb 15, 2023)
19-49881337-G-A		not specified	Uncertain significance (May 08, 2023)
19-49881385-A-G		not specified	Uncertain significance (Feb 06, 2023)
19-49881433-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-49881445-G-A		not specified	Uncertain significance (May 09, 2022)
19-49881456-C-T		not specified	Uncertain significance (May 26, 2024)
19-49881457-G-T		not specified	Uncertain significance (Feb 22, 2023)
19-49882085-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-49882088-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-49882103-C-T		not specified	Uncertain significance (May 17, 2023)
19-49882111-C-T		not specified	Uncertain significance (Dec 19, 2022)
19-49882114-C-G		not specified	Uncertain significance (Mar 24, 2023)
19-49882243-G-A		not specified	Uncertain significance (Mar 21, 2023)
19-49882288-G-T		not specified	Uncertain significance (Apr 18, 2023)
19-49882290-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-49882344-G-A		not specified	Uncertain significance (Jan 05, 2022)
19-49882351-C-T		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D17	protein_coding	protein_coding	ENST00000221543	17	11324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.04e-21	0.00708	125632	0	116	125748	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.152	402	411	0.979	0.0000269	4160
Missense in Polyphen		178	176.35	1.0094		1916
Synonymous	-1.33	197	175	1.13	0.0000119	1313
Loss of Function	0.549	33	36.6	0.902	0.00000193	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00135
Ashkenazi Jewish	0.00	0.00
East Asian	0.000515	0.000489
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000527	0.000519
Middle Eastern	0.000515	0.000489
South Asian	0.000392	0.000392
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable GTPase-activating protein for Rab8; its transient association with Rab8 is mediated by OPTN. Inhibits Rab8-mediated endocytic trafficking, such as of transferrin receptor (TfR) and reduces Rab8 recruitnment to tubules emanating from the endocytic recycling compartment (ERC). Involved in regulation of autophagy. Mediates inhibition of autophagy caused by the OPTN variant GLC1E LYS-50; the function requires its catalytic activity, however, the involved Rab is not known. {ECO:0000269|PubMed:22854040, ECO:0000269|PubMed:24752605}.
• Pathway: Mitophagy - animal - Homo sapiens (human);Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.53

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.282
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d17

Gene ontology

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