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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	79639
Gene name	Transmembrane protein 53
Gene symbol	TMEM53
Synonyms (NCBI Gene)	CTDINET4
Chromosome	1
Chromosome location	1p34.1

188

Show/Hide all (188)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018747	hsa-miR-335-5p	Microarray	18185580
MIRT1437902	hsa-miR-1304	CLIP-seq
MIRT1437903	hsa-miR-186	CLIP-seq
MIRT1437904	hsa-miR-2467-5p	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT1437906	hsa-miR-3133	CLIP-seq
MIRT1437907	hsa-miR-3135	CLIP-seq
MIRT1437908	hsa-miR-3187-3p	CLIP-seq
MIRT1437909	hsa-miR-3188	CLIP-seq
MIRT1437910	hsa-miR-3192	CLIP-seq
MIRT1437911	hsa-miR-3614-5p	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437916	hsa-miR-3975	CLIP-seq
MIRT1437917	hsa-miR-4293	CLIP-seq
MIRT1437918	hsa-miR-4311	CLIP-seq
MIRT1437919	hsa-miR-4325	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT1437921	hsa-miR-4435	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT1437923	hsa-miR-4684-3p	CLIP-seq
MIRT1437924	hsa-miR-4701-5p	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT1437926	hsa-miR-4755-3p	CLIP-seq
MIRT1437927	hsa-miR-4786-5p	CLIP-seq
MIRT1437928	hsa-miR-4797-5p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT1437930	hsa-miR-500a	CLIP-seq
MIRT1437931	hsa-miR-542-3p	CLIP-seq
MIRT1437932	hsa-miR-548s	CLIP-seq
MIRT1437933	hsa-miR-588	CLIP-seq
MIRT1437934	hsa-miR-661	CLIP-seq
MIRT1437935	hsa-miR-759	CLIP-seq
MIRT1437936	hsa-miR-769-5p	CLIP-seq
MIRT1437937	hsa-miR-943	CLIP-seq
MIRT1437902	hsa-miR-1304	CLIP-seq
MIRT1437904	hsa-miR-2467-5p	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT1437909	hsa-miR-3188	CLIP-seq
MIRT1437910	hsa-miR-3192	CLIP-seq
MIRT1437911	hsa-miR-3614-5p	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437916	hsa-miR-3975	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT2131230	hsa-miR-4696	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT2131231	hsa-miR-491-3p	CLIP-seq
MIRT1437934	hsa-miR-661	CLIP-seq
MIRT2352489	hsa-miR-1272	CLIP-seq
MIRT1437902	hsa-miR-1304	CLIP-seq
MIRT1437904	hsa-miR-2467-5p	CLIP-seq
MIRT2352490	hsa-miR-25	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT1437908	hsa-miR-3187-3p	CLIP-seq
MIRT1437909	hsa-miR-3188	CLIP-seq
MIRT1437910	hsa-miR-3192	CLIP-seq
MIRT2352491	hsa-miR-32	CLIP-seq
MIRT1437911	hsa-miR-3614-5p	CLIP-seq
MIRT2352492	hsa-miR-363	CLIP-seq
MIRT2352493	hsa-miR-367	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437916	hsa-miR-3975	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT2352494	hsa-miR-4427	CLIP-seq
MIRT1437921	hsa-miR-4435	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT2352495	hsa-miR-4670-3p	CLIP-seq
MIRT2352496	hsa-miR-4680-3p	CLIP-seq
MIRT1437924	hsa-miR-4701-5p	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT1437930	hsa-miR-500a	CLIP-seq
MIRT1437932	hsa-miR-548s	CLIP-seq
MIRT1437933	hsa-miR-588	CLIP-seq
MIRT1437934	hsa-miR-661	CLIP-seq
MIRT2352497	hsa-miR-92a	CLIP-seq
MIRT2352498	hsa-miR-92b	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT1437910	hsa-miR-3192	CLIP-seq
MIRT1437911	hsa-miR-3614-5p	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT1437930	hsa-miR-500a	CLIP-seq
MIRT1437934	hsa-miR-661	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT1437930	hsa-miR-500a	CLIP-seq
MIRT2646274	hsa-miR-1226	CLIP-seq
MIRT1437902	hsa-miR-1304	CLIP-seq
MIRT2646275	hsa-miR-1324	CLIP-seq
MIRT2646276	hsa-miR-1913	CLIP-seq
MIRT2646277	hsa-miR-1976	CLIP-seq
MIRT1437904	hsa-miR-2467-5p	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT2646278	hsa-miR-3159	CLIP-seq
MIRT2646279	hsa-miR-3166	CLIP-seq
MIRT1437909	hsa-miR-3188	CLIP-seq
MIRT1437910	hsa-miR-3192	CLIP-seq
MIRT2646280	hsa-miR-324-3p	CLIP-seq
MIRT1437911	hsa-miR-3614-5p	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437916	hsa-miR-3975	CLIP-seq
MIRT2646281	hsa-miR-4269	CLIP-seq
MIRT2646282	hsa-miR-4320	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT2646283	hsa-miR-4530	CLIP-seq
MIRT2646284	hsa-miR-4536	CLIP-seq
MIRT2646285	hsa-miR-4643	CLIP-seq
MIRT2646286	hsa-miR-4645-5p	CLIP-seq
MIRT2646287	hsa-miR-4673	CLIP-seq
MIRT2646288	hsa-miR-4722-3p	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT2646289	hsa-miR-4749-3p	CLIP-seq
MIRT2646290	hsa-miR-4778-5p	CLIP-seq
MIRT2646291	hsa-miR-483-3p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT1437930	hsa-miR-500a	CLIP-seq
MIRT2646292	hsa-miR-634	CLIP-seq
MIRT2646293	hsa-miR-642b	CLIP-seq
MIRT2646294	hsa-miR-651	CLIP-seq
MIRT1437934	hsa-miR-661	CLIP-seq
MIRT2646295	hsa-miR-922	CLIP-seq
MIRT2646274	hsa-miR-1226	CLIP-seq
MIRT1437902	hsa-miR-1304	CLIP-seq
MIRT2646275	hsa-miR-1324	CLIP-seq
MIRT2646276	hsa-miR-1913	CLIP-seq
MIRT2646277	hsa-miR-1976	CLIP-seq
MIRT1437904	hsa-miR-2467-5p	CLIP-seq
MIRT1437905	hsa-miR-3122	CLIP-seq
MIRT2646278	hsa-miR-3159	CLIP-seq
MIRT2646279	hsa-miR-3166	CLIP-seq
MIRT1437909	hsa-miR-3188	CLIP-seq
MIRT1437910	hsa-miR-3192	CLIP-seq
MIRT2646280	hsa-miR-324-3p	CLIP-seq
MIRT1437911	hsa-miR-3614-5p	CLIP-seq
MIRT1437912	hsa-miR-3689a-3p	CLIP-seq
MIRT1437913	hsa-miR-3689c	CLIP-seq
MIRT1437914	hsa-miR-3913-5p	CLIP-seq
MIRT1437915	hsa-miR-3929	CLIP-seq
MIRT1437916	hsa-miR-3975	CLIP-seq
MIRT2646281	hsa-miR-4269	CLIP-seq
MIRT2646282	hsa-miR-4320	CLIP-seq
MIRT1437920	hsa-miR-4419b	CLIP-seq
MIRT1437922	hsa-miR-4478	CLIP-seq
MIRT2646283	hsa-miR-4530	CLIP-seq
MIRT2646284	hsa-miR-4536	CLIP-seq
MIRT2646285	hsa-miR-4643	CLIP-seq
MIRT2646286	hsa-miR-4645-5p	CLIP-seq
MIRT2646287	hsa-miR-4673	CLIP-seq
MIRT2646288	hsa-miR-4722-3p	CLIP-seq
MIRT1437925	hsa-miR-4728-5p	CLIP-seq
MIRT2646289	hsa-miR-4749-3p	CLIP-seq
MIRT2646290	hsa-miR-4778-5p	CLIP-seq
MIRT2646291	hsa-miR-483-3p	CLIP-seq
MIRT1437929	hsa-miR-485-5p	CLIP-seq
MIRT1437930	hsa-miR-500a	CLIP-seq
MIRT2646292	hsa-miR-634	CLIP-seq
MIRT2646293	hsa-miR-642b	CLIP-seq
MIRT2646294	hsa-miR-651	CLIP-seq
MIRT1437934	hsa-miR-661	CLIP-seq
MIRT2646295	hsa-miR-922	CLIP-seq

Show/Hide all (14)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005634	Component	Nucleus	IEA
GO:0005640	Component	Nuclear outer membrane	IEA
GO:0005640	Component	Nuclear outer membrane	ISS
GO:0016020	Component	Membrane	IEA
GO:0030279	Process	Negative regulation of ossification	IEA
GO:0030279	Process	Negative regulation of ossification	IMP	33824347
GO:0030514	Process	Negative regulation of BMP signaling pathway	IEA
GO:0030514	Process	Negative regulation of BMP signaling pathway	IMP	33824347
GO:0031965	Component	Nuclear membrane	IDA	33824347
GO:0045668	Process	Negative regulation of osteoblast differentiation	IEA
GO:0045668	Process	Negative regulation of osteoblast differentiation	ISS
GO:0046822	Process	Regulation of nucleocytoplasmic transport	IEA
GO:0046822	Process	Regulation of nucleocytoplasmic transport	IMP	33824347

MIM	HGNC	e!Ensembl
619722	26186	ENSG00000126106

Q6P2H8

Protein name

Transmembrane protein 53 (Nuclear envelope transmembrane protein 4)

Protein function

Ensures normal bone formation, through the negative regulation of bone morphogenetic protein (BMP) signaling in osteoblast lineage cells by blocking cytoplasm-nucleus translocation of phosphorylated SMAD1/5/9 proteins. {ECO:0000269|PubMed:338243

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05705	DUF829	36 → 271	Eukaryotic protein of unknown function (DUF829)	Domain

Tissue specificity

TISSUE SPECIFICITY: [Isoform 1]: Widely expressed. {ECO:0000269|PubMed:33824347}.

Sequence

MASAELDYTIEIPDQPCWSQKNSPSPGGKEAETRQPVVILLGWGGCKDKNLAKYSAIYHK
RGCIVIRYTAPWHMVFFSESLGIPSLRVLAQKLLELLFDYEIEKEPLLFHVFSNGGVMLY
RYVLELLQTRRFCRLRVVGTIFDSAPGDSNLVGALRALAAILERRAAMLRLLLLVAFALV
VVLFHVLLAPITALFHTHFYDRLQDAGSRWPELYLYSRADEVVLARDIERMVEARLARRV
LARSVDFVSSAHVSHLRDYPTYYTSLCVDFMRNCVRC

Sequence length

277

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
Craniotubular dysplasia, Ikegawa type	Pathogenic; Likely pathogenic	rs1644838064, rs1644889088	RCV001822871 RCV001822872	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
TMEM53-related craniotubular dysplasia	Pathogenic; Likely pathogenic	rs1644838064, rs1644889088	RCV001290093 RCV001290094	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (2)

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.
SKELETAL DYSPLASIA	—	GenCC	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TMEM53-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (1)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Hypersensitivity Immediate	Hypersensitivity	Pubtator	39901041	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

TMEM53 (transmembrane protein 53)