TBC1D9 TBC1 domain family member 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBC1D9provided by HGNC
Official Full Name: TBC1 domain family member 9provided by HGNC
Primary source: HGNC:HGNC:21710
See related: Ensembl:ENSG00000109436 MIM:618035; AllianceGenome:HGNC:21710
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MDR1; GRAMD9
Summary: Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in spleen (RPKM 19.8), brain (RPKM 12.2) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q31.21

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (140620782..140756385, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (143940460..144076099, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (141541936..141677539, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TBC1D9 controls TBK1 activation during xenophagy and mitophagy through Ca(2+)-dependent ubiquitin-recognition.TBC1D9 is involved in TBK1 phosphorylation.
Title: TBC1D9 regulates TBK1 activation through Ca(2+) signaling in selective autophagy.
This study concluded that diindolylmethane induces pregnane X receptor -regulated CYP3A4 and MDR1 gene expression.
Title: Diindolylmethane, a naturally occurring compound, induces CYP3A4 and MDR1 gene expression by activating human PXR.
The MDR1 gene CT/TT genotype of C3435T was significantly associated with a shorter progression-free survival (PFS) and overall survival (OS).
Title: MDR1 gene C3435T polymorphism is associated with clinical outcomes in gastric cancer patients treated with postoperative adjuvant chemotherapy.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
CD34+ leukemic subpopulation predominantly displays lower spontaneous apoptosis and has higher expression levels of MDR19TBC1 domain family member 9 (with GRAM domain) ) genes than CD34- cells in childhood AML
Title: CD34+ leukemic subpopulation predominantly displays lower spontaneous apoptosis and has higher expression levels of Bcl-2 and MDR1 genes than CD34- cells in childhood AML.
Plasma levels of atazanavir were significantly higher in patients with MDR1 genotype CC than in those with CT or TT, and bilirubin levels correlated with atazanavir concentrations.
Title: Plasma levels of atazanavir and the risk of hyperbilirubinemia are predicted by the 3435C-->T polymorphism at the multidrug resistance gene 1.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D4S1246 (e-PCR)
- UniSTS:24124

G41967 (e-PCR)
- UniSTS:32580

D4S3312 (e-PCR)
- UniSTS:8529

SHGC-141857 (e-PCR)
- UniSTS:171119

D4S3334 (e-PCR), detects polymorphism
- UniSTS:52883

NoName (e-PCR)
- UniSTS:486560

D4S2601E (e-PCR)
- UniSTS:150991

WI-20032 (e-PCR)
- UniSTS:75741

SHGC-50201 (e-PCR)
- UniSTS:75742

D4S2680 (e-PCR)
- UniSTS:55021

RH92256 (e-PCR)
- UniSTS:90351

RH122866 (e-PCR)
- UniSTS:135163

G19772 (e-PCR)
- UniSTS:58875

A001Y05 (e-PCR)
- UniSTS:58876

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in activation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: TBC1 domain family member 9

Names: TBC1 domain family member 9A; TBC1 domain family, member 9 (with GRAM domain)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_015130.3 → NP_055945.2 TBC1 domain family member 9

See identical proteins and their annotated locations for NP_055945.2

Status: VALIDATED

Source sequence(s)

AC096733, AC108019, AF131785, AI439646, BC038804, BQ308276, CN332501, CN332502

Consensus CDS

CCDS47136.1

UniProtKB/Swiss-Prot

A6H8U8, D3DNZ1, O94958, Q6ZT07

Related

ENSP00000411197.2, ENST00000442267.3

Conserved Domains (4) summary

smart00164
Location:512 → 722

TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

cd13354
Location:304 → 399

PH-GRAM2_TCB1D9_TCB1D9B; TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2

cd13351
Location:157 → 255

PH-GRAM1_TCB1D9_TCB1D9B; TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1

cl08302
Location:893 → 923

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...