TBC1D9

TBC1 domain family member 9, the group of GRAM domain containing|EF-hand domain containing

Basic information

Region (hg38): 4:140620782-140756385

Links

ENSG00000109436 ∙ NCBI:23158 ∙ OMIM:618035 ∙ HGNC:21710 ∙ Uniprot:Q6ZT07 ∙ 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 TBC1D9 gene.

• not_specified (106 variants)
• not_provided (4 variants)
• Attention_deficit_hyperactivity_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015130.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			105	1		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	105	3	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBC1D9	protein_coding	protein_coding	ENST00000442267	21	135356

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000280	1.00	124662	0	29	124691	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.16	483	722	0.669	0.0000416	8332
Missense in Polyphen		217	374.13	0.58001		4411
Synonymous	0.978	268	289	0.927	0.0000175	2404
Loss of Function	4.69	19	57.3	0.332	0.00000291	687

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.0000556	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.000198	0.000195
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000657	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein for Rab family protein(s).

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.266
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.68

Haploinsufficiency Scores

• pHI: 0.253
• hipred: Y
• hipred_score: 0.639
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbc1d9

Gene ontology

• Biological process: intracellular protein transport;activation of GTPase activity
• Cellular component: cell
• Molecular function: GTPase activator activity;calcium ion binding;protein binding;Rab GTPase binding