TBC1D14

TBC1 domain family member 14

Basic information

Region (hg38): 4:6909241-7033118

Links

ENSG00000132405 ∙ NCBI:57533 ∙ OMIM:614855 ∙ HGNC:29246 ∙ Uniprot:Q9P2M4 ∙ 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 TBC1D14 gene.

• Inborn genetic diseases (24 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D14 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	1
missense			22	2	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	2

Variants in TBC1D14

This is a list of pathogenic ClinVar variants found in the TBC1D14 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-6923403-A-G		not specified	Uncertain significance (Dec 07, 2021)
4-6923421-A-G		not specified	Uncertain significance (Jul 11, 2023)
4-6923449-T-G		not specified	Uncertain significance (Sep 17, 2021)
4-6923486-G-A			Benign (Aug 15, 2017)
4-6923516-G-C		not specified	Uncertain significance (Oct 20, 2023)
4-6923517-C-T		not specified	Uncertain significance (Oct 20, 2021)
4-6923586-C-T		not specified	Uncertain significance (Jan 31, 2023)
4-6923637-C-T		not specified	Likely benign (Mar 01, 2023)
4-6923642-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-6923644-C-T			Benign (Aug 15, 2017)
4-6923649-G-A		not specified	Likely benign (Oct 03, 2022)
4-6923658-A-G		not specified	Uncertain significance (Dec 08, 2023)
4-6923694-A-G		not specified	Uncertain significance (Jun 02, 2023)
4-6923705-G-A		not specified	Uncertain significance (Apr 07, 2023)
4-6923721-C-T		not specified	Uncertain significance (Jan 10, 2023)
4-6923741-A-C		not specified	Uncertain significance (Aug 17, 2022)
4-6923747-C-T		not specified	Uncertain significance (Jul 26, 2022)
4-6923799-C-T		not specified	Uncertain significance (Dec 19, 2023)
4-6923801-G-C		not specified	Uncertain significance (Aug 02, 2021)
4-6923814-G-A		not specified	Uncertain significance (Nov 22, 2022)
4-6923853-C-T		not specified	Uncertain significance (Oct 28, 2023)
4-6923864-G-A		not specified	Uncertain significance (Feb 10, 2022)
4-6923924-G-C		not specified	Uncertain significance (Dec 17, 2023)
4-6967348-A-G		not specified	Likely benign (Dec 27, 2023)
4-6967360-G-C		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D14	protein_coding	protein_coding	ENST00000409757	13	123877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0393	0.961	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	346	413	0.838	0.0000257	4576
Missense in Polyphen		93	162.52	0.57223		1877
Synonymous	-1.11	189	171	1.11	0.0000120	1342
Loss of Function	4.12	10	37.1	0.270	0.00000232	377

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of starvation-induced autophagosome formation. {ECO:0000269|PubMed:22613832}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.98

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.488
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.618

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d14
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: intracellular protein transport;negative regulation of autophagy;recycling endosome to Golgi transport;activation of GTPase activity;regulation of cilium assembly;regulation of autophagosome assembly
• Cellular component: nucleoplasm;autophagosome;Golgi apparatus;cytosol;intracellular membrane-bounded organelle;recycling endosome
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding;protein kinase binding