TBC1D25

TBC1 domain family member 25

Basic information

Region (hg38): X:48539714-48562609

Previous symbols: [ "OATL1" ]

Links

ENSG00000068354 ∙ NCBI:4943 ∙ OMIM:311240 ∙ HGNC:8092 ∙ Uniprot:Q3MII6 ∙ 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 TBC1D25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D25 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				2		2
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in TBC1D25

This is a list of pathogenic ClinVar variants found in the TBC1D25 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48539907-G-A			Uncertain significance (Jun 01, 2024)
X-48541358-A-C			Uncertain significance (Sep 30, 2021)
X-48544901-G-A		not specified	Uncertain significance (May 09, 2023)
X-48544904-A-G		not specified	Uncertain significance (Apr 27, 2022)
X-48544944-C-A		not specified	Uncertain significance (Feb 26, 2024)
X-48544997-G-A		not specified	Uncertain significance (Feb 13, 2023)
X-48545020-G-A		not specified	Uncertain significance (Apr 26, 2023)
X-48558901-A-G			Likely benign (Apr 01, 2022)
X-48558992-G-A		not specified	Uncertain significance (Jun 10, 2024)
X-48559623-C-T		not specified	Uncertain significance (Oct 06, 2022)
X-48559686-C-T		not specified	Uncertain significance (Mar 16, 2022)
X-48559735-C-T		not specified	Uncertain significance (Feb 10, 2023)
X-48559843-G-A		not specified	Uncertain significance (May 26, 2024)
X-48559984-T-C		not specified	Uncertain significance (Oct 21, 2021)
X-48560053-T-G		Abnormality of neuronal migration	Benign (Oct 31, 2014)
X-48560259-C-G		not specified	Uncertain significance (Sep 06, 2022)
X-48560291-G-C		not specified	Uncertain significance (Jan 04, 2024)
X-48560433-G-A		not specified	Uncertain significance (Jan 03, 2024)
X-48560489-G-A			Likely benign (Feb 01, 2023)
X-48560502-G-A		not specified	Uncertain significance (Oct 06, 2023)
X-48560509-T-C		not specified	Uncertain significance (May 24, 2024)
X-48560559-C-T		not specified	Uncertain significance (May 14, 2024)
X-48560746-G-A		not specified	Uncertain significance (Oct 12, 2021)
X-48560893-G-A		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D25	protein_coding	protein_coding	ENST00000376771	6	23153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.523	0.477	125736	2	3	125741	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.10	149	300	0.496	0.0000266	4415
Missense in Polyphen		38	133.88	0.28384		1955
Synonymous	0.925	115	128	0.896	0.0000111	1504
Loss of Function	3.24	4	19.4	0.206	0.00000181	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000763	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000502	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a GTPase-activating protein specific for RAB33B. Involved in the regulation of autophagosome maturation, the process in which autophagosomes fuse with endosomes and lysosomes. {ECO:0000269|PubMed:21383079}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.357
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.524
• hipred: Y
• hipred_score: 0.662
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.549

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d25

Gene ontology

• Biological process: intracellular protein transport;autophagy;activation of GTPase activity;regulation of autophagosome maturation
• Cellular component: autophagosome;cytoplasmic vesicle
• Molecular function: GTPase activator activity;protein binding;Rab GTPase binding