TBC1D9B TBC1 domain family member 9B [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBC1D9Bprovided by HGNC
Official Full Name: TBC1 domain family member 9Bprovided by HGNC
Primary source: HGNC:HGNC:29097
See related: Ensembl:ENSG00000197226 MIM:618039; AllianceGenome:HGNC:29097
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: GRAMD9B
Summary: Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in fat (RPKM 32.0), thyroid (RPKM 25.0) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 5q35.3

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (179862071..179907897, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (180417215..180462876, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (179289071..179334897, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study found that TBC1D9B, a GTPase activating protein for RAB11A, interacted with LC3B. TBC1D9B could also interact with other mammalian ATG8 homologues and revealed that TBC1D9B can positively regulate autophagic flux, possibly through its GTPase activity to inactivate RAB11A, facilitating the proper destination of the autophagosomes to the degradation.
Title: Interaction of TBC1D9B with Mammalian ATG8 Homologues Regulates Autophagic Flux.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

bac51950T (e-PCR)
- UniSTS:181528

D5S2217E (e-PCR)
- UniSTS:154423

RH94087 (e-PCR)
- UniSTS:92476

D5S2232E (e-PCR)
- UniSTS:154438

SGC34653 (e-PCR)
- UniSTS:21605

D5S2285E (e-PCR)
- UniSTS:154491

D5S2295E (e-PCR)
- UniSTS:154503

WI-20921 (e-PCR)
- UniSTS:76479

WIAF-2213 (e-PCR)
- UniSTS:50159

Homology

Homologs of the TBC1D9B gene: The TBC1D9B gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, and frog.
Orthologs from Annotation Pipeline: 474 organisms have orthologs with human gene TBC1D9B
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
NOT involved_in regulation of cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: TBC1 domain family member 9B

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

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_015043.4 → NP_055858.2 TBC1 domain family member 9B isoform b

See identical proteins and their annotated locations for NP_055858.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame coding exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC008393, AC010285

Consensus CDS

CCDS4450.1

UniProtKB/Swiss-Prot

Q66K14

UniProtKB/TrEMBL

B3KM54

Related

ENSP00000347375.3, ENST00000355235.8

Conserved Domains (4) summary

smart00164
Location:505 → 715

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

cd13354
Location:299 → 394

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:153 → 251

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:855 → 906

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 ...
NM_198868.3 → NP_942568.2 TBC1 domain family member 9B isoform a

See identical proteins and their annotated locations for NP_942568.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AC008393, AC010285

Consensus CDS

CCDS43408.1

UniProtKB/Swiss-Prot

Q66K14, Q96H49

UniProtKB/TrEMBL

B3KM54, Q9BW24

Related

ENSP00000349291.3, ENST00000356834.7

Conserved Domains (4) summary

smart00164
Location:505 → 715

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

cd13354
Location:299 → 394

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:153 → 251

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:855 → 906

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 ...