Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	55773
Gene name	TBC1 domain family member 23
Gene symbol	TBC1D23
Synonyms (NCBI Gene)	NS4ATP1PCH11
Chromosome	3
Chromosome location	3q12.1-q12.2

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1553730885	T>AA	Pathogenic	Frameshift variant, coding sequence variant
rs1553731603	G>A	Pathogenic	Splice donor variant
rs1553731605	T>A	Pathogenic	Splice donor variant

204

Show/Hide all (204)

miRTarBase ID	miRNA	Experiments
MIRT1412767	hsa-miR-3684	CLIP-seq
MIRT1412768	hsa-miR-4503	CLIP-seq
MIRT1412769	hsa-miR-1207-5p	CLIP-seq
MIRT1412770	hsa-miR-190	CLIP-seq
MIRT1412771	hsa-miR-190b	CLIP-seq
MIRT1412772	hsa-miR-202	CLIP-seq
MIRT1412773	hsa-miR-204	CLIP-seq
MIRT1412774	hsa-miR-211	CLIP-seq
MIRT1412775	hsa-miR-217	CLIP-seq
MIRT1412776	hsa-miR-297	CLIP-seq
MIRT1412777	hsa-miR-3177-5p	CLIP-seq
MIRT1412778	hsa-miR-3189-5p	CLIP-seq
MIRT1412779	hsa-miR-323b-5p	CLIP-seq
MIRT1412780	hsa-miR-3609	CLIP-seq
MIRT1412781	hsa-miR-3646	CLIP-seq
MIRT1412782	hsa-miR-3686	CLIP-seq
MIRT1412783	hsa-miR-3924	CLIP-seq
MIRT1412784	hsa-miR-4323	CLIP-seq
MIRT1412785	hsa-miR-4433	CLIP-seq
MIRT1412786	hsa-miR-4459	CLIP-seq
MIRT1412768	hsa-miR-4503	CLIP-seq
MIRT1412787	hsa-miR-4704-3p	CLIP-seq
MIRT1412788	hsa-miR-4716-5p	CLIP-seq
MIRT1412789	hsa-miR-4736	CLIP-seq
MIRT1412790	hsa-miR-4753-3p	CLIP-seq
MIRT1412791	hsa-miR-4755-5p	CLIP-seq
MIRT1412792	hsa-miR-4763-3p	CLIP-seq
MIRT1412793	hsa-miR-4768-3p	CLIP-seq
MIRT1412794	hsa-miR-4768-5p	CLIP-seq
MIRT1412795	hsa-miR-4775	CLIP-seq
MIRT1412796	hsa-miR-4778-5p	CLIP-seq
MIRT1412797	hsa-miR-511	CLIP-seq
MIRT1412798	hsa-miR-548ah	CLIP-seq
MIRT1412799	hsa-miR-567	CLIP-seq
MIRT1412800	hsa-miR-582-5p	CLIP-seq
MIRT1412801	hsa-miR-623	CLIP-seq
MIRT1412802	hsa-miR-640	CLIP-seq
MIRT1412803	hsa-miR-885-5p	CLIP-seq
MIRT1412778	hsa-miR-3189-5p	CLIP-seq
MIRT1412781	hsa-miR-3646	CLIP-seq
MIRT2123958	hsa-miR-4276	CLIP-seq
MIRT1412784	hsa-miR-4323	CLIP-seq
MIRT1412768	hsa-miR-4503	CLIP-seq
MIRT2123959	hsa-miR-4735-5p	CLIP-seq
MIRT1412795	hsa-miR-4775	CLIP-seq
MIRT2123960	hsa-miR-590-3p	CLIP-seq
MIRT2346053	hsa-miR-3662	CLIP-seq
MIRT2346054	hsa-miR-3672	CLIP-seq
MIRT2638933	hsa-miR-1236	CLIP-seq
MIRT2638934	hsa-miR-1256	CLIP-seq
MIRT2638935	hsa-miR-1265	CLIP-seq
MIRT2638936	hsa-miR-1271	CLIP-seq
MIRT2638937	hsa-miR-1297	CLIP-seq
MIRT2638938	hsa-miR-155	CLIP-seq
MIRT2638939	hsa-miR-182	CLIP-seq
MIRT1412770	hsa-miR-190	CLIP-seq
MIRT1412771	hsa-miR-190b	CLIP-seq
MIRT2638940	hsa-miR-2053	CLIP-seq
MIRT2638941	hsa-miR-2392	CLIP-seq
MIRT2638942	hsa-miR-26a	CLIP-seq
MIRT2638943	hsa-miR-26b	CLIP-seq
MIRT2638944	hsa-miR-2909	CLIP-seq
MIRT1412776	hsa-miR-297	CLIP-seq
MIRT2638945	hsa-miR-3074-3p	CLIP-seq
MIRT2638946	hsa-miR-3129-3p	CLIP-seq
MIRT2638947	hsa-miR-3140-3p	CLIP-seq
MIRT2638948	hsa-miR-3148	CLIP-seq
MIRT2638949	hsa-miR-3158-5p	CLIP-seq
MIRT2638950	hsa-miR-3163	CLIP-seq
MIRT2638951	hsa-miR-3175	CLIP-seq
MIRT1412777	hsa-miR-3177-5p	CLIP-seq
MIRT2638952	hsa-miR-3201	CLIP-seq
MIRT2638953	hsa-miR-342-5p	CLIP-seq
MIRT2346054	hsa-miR-3672	CLIP-seq
MIRT2638954	hsa-miR-3675-3p	CLIP-seq
MIRT2638955	hsa-miR-3681	CLIP-seq
MIRT2638956	hsa-miR-3908	CLIP-seq
MIRT2638957	hsa-miR-3920	CLIP-seq
MIRT2638958	hsa-miR-3921	CLIP-seq
MIRT1412783	hsa-miR-3924	CLIP-seq
MIRT2638959	hsa-miR-3936	CLIP-seq
MIRT2638960	hsa-miR-3942-5p	CLIP-seq
MIRT2638961	hsa-miR-410	CLIP-seq
MIRT2638962	hsa-miR-4263	CLIP-seq
MIRT2638963	hsa-miR-4275	CLIP-seq
MIRT2123958	hsa-miR-4276	CLIP-seq
MIRT2638964	hsa-miR-4278	CLIP-seq
MIRT2638965	hsa-miR-4282	CLIP-seq
MIRT2638966	hsa-miR-4318	CLIP-seq
MIRT2638967	hsa-miR-4328	CLIP-seq
MIRT2638968	hsa-miR-4418	CLIP-seq
MIRT2638969	hsa-miR-4423-5p	CLIP-seq
MIRT2638970	hsa-miR-4465	CLIP-seq
MIRT2638971	hsa-miR-4477b	CLIP-seq
MIRT2638972	hsa-miR-4480	CLIP-seq
MIRT2638973	hsa-miR-4509	CLIP-seq
MIRT2638974	hsa-miR-452	CLIP-seq
MIRT2638975	hsa-miR-4642	CLIP-seq
MIRT2638976	hsa-miR-4653-5p	CLIP-seq
MIRT2638977	hsa-miR-4664-5p	CLIP-seq
MIRT2638978	hsa-miR-4668-5p	CLIP-seq
MIRT2638979	hsa-miR-4670-3p	CLIP-seq
MIRT2638980	hsa-miR-4676-3p	CLIP-seq
MIRT2638981	hsa-miR-4693-5p	CLIP-seq
MIRT2638982	hsa-miR-4698	CLIP-seq
MIRT2638983	hsa-miR-4703-5p	CLIP-seq
MIRT2638984	hsa-miR-4709-5p	CLIP-seq
MIRT2638985	hsa-miR-4729	CLIP-seq
MIRT2123959	hsa-miR-4735-5p	CLIP-seq
MIRT2638986	hsa-miR-4744	CLIP-seq
MIRT2638987	hsa-miR-4766-3p	CLIP-seq
MIRT1412795	hsa-miR-4775	CLIP-seq
MIRT1412796	hsa-miR-4778-5p	CLIP-seq
MIRT2638988	hsa-miR-4781-3p	CLIP-seq
MIRT2638989	hsa-miR-4791	CLIP-seq
MIRT2638990	hsa-miR-4799-5p	CLIP-seq
MIRT2638991	hsa-miR-500a	CLIP-seq
MIRT2638992	hsa-miR-501-3p	CLIP-seq
MIRT2638993	hsa-miR-502-3p	CLIP-seq
MIRT2638994	hsa-miR-509-3-5p	CLIP-seq
MIRT2638995	hsa-miR-509-5p	CLIP-seq
MIRT2638996	hsa-miR-513a-3p	CLIP-seq
MIRT2638997	hsa-miR-548g	CLIP-seq
MIRT1412799	hsa-miR-567	CLIP-seq
MIRT2638998	hsa-miR-569	CLIP-seq
MIRT2638999	hsa-miR-576-5p	CLIP-seq
MIRT1412800	hsa-miR-582-5p	CLIP-seq
MIRT2123960	hsa-miR-590-3p	CLIP-seq
MIRT1412802	hsa-miR-640	CLIP-seq
MIRT2639000	hsa-miR-651	CLIP-seq
MIRT2639001	hsa-miR-892a	CLIP-seq
MIRT2639002	hsa-miR-96	CLIP-seq
MIRT2638933	hsa-miR-1236	CLIP-seq
MIRT2638934	hsa-miR-1256	CLIP-seq
MIRT2638936	hsa-miR-1271	CLIP-seq
MIRT2638938	hsa-miR-155	CLIP-seq
MIRT2638939	hsa-miR-182	CLIP-seq
MIRT1412770	hsa-miR-190	CLIP-seq
MIRT1412771	hsa-miR-190b	CLIP-seq
MIRT2638940	hsa-miR-2053	CLIP-seq
MIRT2638944	hsa-miR-2909	CLIP-seq
MIRT1412776	hsa-miR-297	CLIP-seq
MIRT2638946	hsa-miR-3129-3p	CLIP-seq
MIRT2638947	hsa-miR-3140-3p	CLIP-seq
MIRT2638948	hsa-miR-3148	CLIP-seq
MIRT2638949	hsa-miR-3158-5p	CLIP-seq
MIRT2638950	hsa-miR-3163	CLIP-seq
MIRT2638951	hsa-miR-3175	CLIP-seq
MIRT1412777	hsa-miR-3177-5p	CLIP-seq
MIRT2638952	hsa-miR-3201	CLIP-seq
MIRT2638953	hsa-miR-342-5p	CLIP-seq
MIRT1412780	hsa-miR-3609	CLIP-seq
MIRT2346054	hsa-miR-3672	CLIP-seq
MIRT2638954	hsa-miR-3675-3p	CLIP-seq
MIRT2638955	hsa-miR-3681	CLIP-seq
MIRT2638956	hsa-miR-3908	CLIP-seq
MIRT2638957	hsa-miR-3920	CLIP-seq
MIRT2638958	hsa-miR-3921	CLIP-seq
MIRT1412783	hsa-miR-3924	CLIP-seq
MIRT2638959	hsa-miR-3936	CLIP-seq
MIRT2638960	hsa-miR-3942-5p	CLIP-seq
MIRT2638961	hsa-miR-410	CLIP-seq
MIRT2638962	hsa-miR-4263	CLIP-seq
MIRT2638963	hsa-miR-4275	CLIP-seq
MIRT2123958	hsa-miR-4276	CLIP-seq
MIRT2638964	hsa-miR-4278	CLIP-seq
MIRT2638965	hsa-miR-4282	CLIP-seq
MIRT2638966	hsa-miR-4318	CLIP-seq
MIRT2638967	hsa-miR-4328	CLIP-seq
MIRT2638968	hsa-miR-4418	CLIP-seq
MIRT2638971	hsa-miR-4477b	CLIP-seq
MIRT2638972	hsa-miR-4480	CLIP-seq
MIRT2638973	hsa-miR-4509	CLIP-seq
MIRT2638974	hsa-miR-452	CLIP-seq
MIRT2638975	hsa-miR-4642	CLIP-seq
MIRT2638976	hsa-miR-4653-5p	CLIP-seq
MIRT2638977	hsa-miR-4664-5p	CLIP-seq
MIRT2638978	hsa-miR-4668-5p	CLIP-seq
MIRT2638980	hsa-miR-4676-3p	CLIP-seq
MIRT2638981	hsa-miR-4693-5p	CLIP-seq
MIRT2638982	hsa-miR-4698	CLIP-seq
MIRT2638983	hsa-miR-4703-5p	CLIP-seq
MIRT2638984	hsa-miR-4709-5p	CLIP-seq
MIRT2638985	hsa-miR-4729	CLIP-seq
MIRT2123959	hsa-miR-4735-5p	CLIP-seq
MIRT2638986	hsa-miR-4744	CLIP-seq
MIRT2638987	hsa-miR-4766-3p	CLIP-seq
MIRT1412795	hsa-miR-4775	CLIP-seq
MIRT1412796	hsa-miR-4778-5p	CLIP-seq
MIRT2638989	hsa-miR-4791	CLIP-seq
MIRT2638990	hsa-miR-4799-5p	CLIP-seq
MIRT2638994	hsa-miR-509-3-5p	CLIP-seq
MIRT2638995	hsa-miR-509-5p	CLIP-seq
MIRT2638996	hsa-miR-513a-3p	CLIP-seq
MIRT1412798	hsa-miR-548ah	CLIP-seq
MIRT2638997	hsa-miR-548g	CLIP-seq
MIRT1412799	hsa-miR-567	CLIP-seq
MIRT2638998	hsa-miR-569	CLIP-seq
MIRT2638999	hsa-miR-576-5p	CLIP-seq
MIRT1412800	hsa-miR-582-5p	CLIP-seq
MIRT2123960	hsa-miR-590-3p	CLIP-seq
MIRT1412802	hsa-miR-640	CLIP-seq
MIRT2639001	hsa-miR-892a	CLIP-seq
MIRT2639002	hsa-miR-96	CLIP-seq

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25416956, 29084197, 32296183, 32814053
GO:0005794	Component	Golgi apparatus	IDA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005802	Component	Trans-Golgi network	IBA
GO:0005802	Component	Trans-Golgi network	IDA	28823706, 29084197, 29426865
GO:0005829	Component	Cytosol	IEA
GO:0007399	Process	Nervous system development	IEA
GO:0007420	Process	Brain development	IMP	28823706, 28823707
GO:0016192	Process	Vesicle-mediated transport	ISS
GO:0031175	Process	Neuron projection development	ISS
GO:0031410	Component	Cytoplasmic vesicle	IDA	29426865
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IBA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IMP	29084197
GO:0048513	Process	Animal organ development	IEA
GO:0071203	Component	WASH complex	IDA	29084197
GO:0099041	Process	Vesicle tethering to Golgi	IBA
GO:0099041	Process	Vesicle tethering to Golgi	IDA	29426865
GO:1990403	Process	Embryonic brain development	IBA
GO:1990403	Process	Embryonic brain development	ISS

MIM	HGNC	e!Ensembl
617687	25622	ENSG00000036054

Q9NUY8

Protein name

TBC1 domain family member 23 (HCV non-structural protein 4A-transactivated protein 1)

Protein function

Putative Rab GTPase-activating protein which plays a role in vesicular trafficking (PubMed:28823707). Involved in endosome-to-Golgi trafficking. Acts as a bridging protein by binding simultaneously to golgins, including GOLGA1 and GOLGA4, locate

PDB

6JL7 , 6JM5 , 8JJ9 , 8QQF

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00566	RabGAP-TBC	47 → 246	Rab-GTPase-TBC domain	Family
PF00581	Rhodanese	323 → 440	Rhodanese-like domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Isoform 1: Widely expressed, including in fetal adult brain (corpus callosum, pons, cerebellum), spinal cord, heart, skeletal muscle, thymus and bone marrow, and at lower levels in spleen. Hardly detected in liver, kidney, colon and te

Sequence

MAEGEDVPPLPTSSGDGWEKDLEEALEAGGCDLETLRNIIQGRPLPADLRAKVWKIALNV
AGKGDSLASWDGILDLPEQNTIHKDCLQFIDQLSVPEEKAAELLLDIESVITFYCKSRNI
KYSTSLSWIHLLKPLVHLQLPRSDLYNCFYAIMNKYIPRDCSQKGRPFHLFRLLIQYHEP
ELCSYLDTKKITPDSYALNWLGSLFACYCSTEVTQAIWDGYLQQADPFFIYFLMLIILVN
AKEVILTQESDSKEEVIKFLENTPSSLNIEDIEDLFSLAQYYCSKTPASFRKDNHHLFGS
TLLGIKDDDADLSQALCLAISVSEILQANQLQGEGVRFFVVDCRPAEQYNAGHLSTAFHL
DSDLMLQNPSEFAQSVKSLLEAQKQSIESGSIAGGEHLCFMGSGREEEDMYMNMVLAHFL
QKNKEYVSIASGGFMALQQHLADINVDGPENGYGHWIASTSGSRSSINSVDGESPNGSSD
RGMKSLVNKMTVALKTKSVNVREKVISFIENTSTPVDRMSFNLPWPDRSCTERHVSSSDR
VGKPYRGVKPVFSIGDEEEYDTDEIDSSSMSDDDRKEVVNIQTWINKPDVKHHFPCKEVK
ESGHMFPSHLLVTATHMYCLREIVSRKGLAYIQSRQALNSVVKITSKKKHPELITFKYGN
SSASGIEILAIERYLIPNAGDATKAIKQQIMKVLDALES

Sequence length

699

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Pontocerebellar hypoplasia, type 11	Likely pathogenic; Pathogenic	rs1354130291, rs2148863572, rs2148861371, rs2472195074, rs1553730872, rs1553730885, rs1553731605, rs1553731603, rs773150360	RCV001785049 RCV001785050 RCV001783847 RCV003229782 RCV000508996 View all (6 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontoneocerebellar hypoplasia	Pathogenic	rs1553730872, rs1553730885, rs1553731605	RCV000515777 RCV000515789 RCV000515797	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
CENTRAL NERVOUS SYSTEM CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TBC1D23-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (23)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital pontocerebellar hypoplasia	Pontoneocerebellar hypoplasia	BEFREE	28823706, 28823707, 31624125		★★★★★ ★☆☆☆☆ Found in Text Mining only
Deglutition Disorders	Dysphagia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hyperopia	Hyperopia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	28397838		★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	28823707		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Pontocerebellar Hypoplasia Type 2	Pontocerebellar hypoplasia	Pubtator	36076253	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
PONTOCEREBELLAR HYPOPLASIA, TYPE 11	Pontocerebellar hypoplasia	GENOMICS_ENGLAND_DG	28397838		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PONTOCEREBELLAR HYPOPLASIA, TYPE 11	Pontocerebellar hypoplasia	UNIPROT_DG	28823706, 28823707		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PONTOCEREBELLAR HYPOPLASIA, TYPE 11	Pontocerebellar hypoplasia	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontoneocerebellar hypoplasia	Pontoneocerebellar hypoplasia	BEFREE	28823706, 28823707, 31624125		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Pontoneocerebellar hypoplasia	Pontoneocerebellar hypoplasia	CLINVAR_DG	28823707		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe intellectual disability	Mental retardation	BEFREE	28823707		★★★★★ ★☆☆☆☆ Found in Text Mining only
Severe intellectual disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Stereotyped Behavior	Stereotyped Behavior	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

TBC1D23 (TBC1 domain family member 23)