TBC1D30

TBC1 domain family member 30

Basic information

Region (hg38): 12:64759484-64881033

Links

ENSG00000111490 ∙ NCBI:23329 ∙ OMIM:615077 ∙ HGNC:29164 ∙ Uniprot:Q9Y2I9 ∙ 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 TBC1D30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D30 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			30	3	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding					2	2
Total	0	0	31	4	3

Variants in TBC1D30

This is a list of pathogenic ClinVar variants found in the TBC1D30 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-64759493-T-C			Benign (Jun 28, 2018)
12-64759540-GGGGCGGAGAACCGGAGAAAA-G			Benign (Jun 19, 2018)
12-64824949-G-A		not specified	Uncertain significance (Jan 10, 2022)
12-64830438-T-C		not specified	Uncertain significance (Mar 16, 2022)
12-64832141-G-A		not specified	Uncertain significance (Dec 05, 2022)
12-64832208-C-T			Likely benign (Nov 01, 2022)
12-64832279-A-G		not specified	Uncertain significance (Dec 28, 2022)
12-64832293-G-A		not specified	Uncertain significance (Jun 04, 2024)
12-64836489-G-T			Uncertain significance (Jan 29, 2018)
12-64836523-G-A		not specified	Uncertain significance (May 28, 2024)
12-64836527-G-A		not specified	Uncertain significance (Apr 08, 2022)
12-64836539-A-G		not specified	Uncertain significance (Apr 18, 2024)
12-64836589-A-G		not specified	Uncertain significance (Dec 12, 2022)
12-64836626-C-T		not specified	Uncertain significance (Apr 16, 2024)
12-64836645-C-G		not specified	Uncertain significance (May 15, 2023)
12-64838704-C-T		not specified	Uncertain significance (Feb 10, 2022)
12-64838718-A-G		not specified	Uncertain significance (Apr 28, 2022)
12-64843445-T-C		not specified	Uncertain significance (Jan 24, 2024)
12-64864729-C-A		not specified	Uncertain significance (Dec 07, 2023)
12-64864755-A-G		not specified	Uncertain significance (Apr 29, 2024)
12-64864779-G-C		not specified	Uncertain significance (Dec 01, 2022)
12-64866757-T-A			Benign (Feb 20, 2018)
12-64866825-G-A		not specified	Uncertain significance (May 17, 2023)
12-64866880-A-C		not specified	Uncertain significance (Aug 16, 2021)
12-64870677-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D30	protein_coding	protein_coding	ENST00000539867	12	100224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.889	0.111	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	259	414	0.626	0.0000217	4987
Missense in Polyphen		92	164.5	0.55927		2107
Synonymous	2.47	125	165	0.756	0.00000967	1483
Loss of Function	4.41	6	33.6	0.179	0.00000189	391

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase-activating protein (GAP) with broad specificity. Acts as a GAP for RAB3A. Also exhibits significant GAP activity toward RAB22A, RAB27A, and RAB35 in vitro.

Haploinsufficiency Scores

• pHI: 0.273
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d30

Gene ontology

• Biological process: intracellular protein transport;positive regulation of GTPase activity;activation of GTPase activity;negative regulation of cilium assembly
• Cellular component: cytosol;plasma membrane;cilium;ciliary basal body
• Molecular function: GTPase activator activity;Rab GTPase binding