SEC16B (SEC16 homolog B, endoplasmic reticulum export factor)

Download as csv Download as pdf

Log in to save this analysis

Save This Analysis

Title Project / Tag (optional) Note (optional)

Cancel Save

On this page

Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 89866
• Gene name: SEC16 homolog B, endoplasmic reticulum export factor
• Gene symbol: SEC16B
• Synonyms (NCBI Gene): LZTR2, PGPR-p117, RGPR, RGPR-p117, SEC16S
• Chromosome: 1
• Chromosome location: 1q25.2
• Summary: SEC16B is a mammalian homolog of S. cerevisiae Sec16 that is required for organization of transitional endoplasmic reticulum (ER) sites and protein export (Bhattacharyya and Glick, 2007 [PubMed 17192411]).[supplied by OMIM, Jun 2009]

miRNA Show/Hide all (20)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017884	hsa-miR-335-5p	Microarray	18185580
MIRT1332491	hsa-miR-3184	CLIP-seq
MIRT1332492	hsa-miR-3192	CLIP-seq
MIRT1332493	hsa-miR-3529	CLIP-seq
MIRT1332494	hsa-miR-379	CLIP-seq
MIRT1332495	hsa-miR-423-5p	CLIP-seq
MIRT1332496	hsa-miR-4451	CLIP-seq
MIRT1332497	hsa-miR-4492	CLIP-seq
MIRT1332498	hsa-miR-4498	CLIP-seq
MIRT1332499	hsa-miR-4505	CLIP-seq
MIRT1332500	hsa-miR-4650-3p	CLIP-seq
MIRT1332501	hsa-miR-762	CLIP-seq
MIRT2323007	hsa-miR-3163	CLIP-seq
MIRT2323008	hsa-miR-3942-5p	CLIP-seq
MIRT2323009	hsa-miR-4703-5p	CLIP-seq
MIRT2394145	hsa-miR-3607-5p	CLIP-seq
MIRT2394146	hsa-miR-3944-5p	CLIP-seq
MIRT2394147	hsa-miR-4639-3p	CLIP-seq
MIRT2394148	hsa-miR-668	CLIP-seq
MIRT2394149	hsa-miR-767-3p	CLIP-seq

Gene ontology (GO) Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 21478858, 22355596, 25416956, 28514442, 33961781
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	IMP	21478858
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	TAS	22355596
GO:0007029	Process	Endoplasmic reticulum organization	IDA	21768384
GO:0007030	Process	Golgi organization	IBA
GO:0007031	Process	Peroxisome organization	IDA	21768384
GO:0007031	Process	Peroxisome organization	IEA
GO:0010628	Process	Positive regulation of gene expression	IMP	21768384
GO:0012507	Component	ER to Golgi transport vesicle membrane	IBA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0016559	Process	Peroxisome fission	IMP	21768384
GO:0043231	Component	Intracellular membrane-bounded organelle	IDA	21768384
GO:0070863	Process	Positive regulation of protein exit from endoplasmic reticulum	IMP	21768384
GO:0070971	Component	Endoplasmic reticulum exit site	IBA
GO:0070971	Component	Endoplasmic reticulum exit site	IDA	21478858, 22355596
GO:0070971	Component	Endoplasmic reticulum exit site	IEA
GO:0070973	Process	Protein localization to endoplasmic reticulum exit site	IBA

Other IDs

• MIM: 612855
• HGNC: 30301
• e!Ensembl: ENSG00000120341

Protein

• UniProt ID: Q96JE7
• Protein name: Protein transport protein Sec16B (Leucine zipper transcription regulator 2) (Regucalcin gene promoter region-related protein p117) (RGPR-p117) (SEC16 homolog B)
• Protein function: Plays a role in the organization of the endoplasmic reticulum exit sites (ERES), also known as transitional endoplasmic reticulum (tER). Required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus (PubMed:17192411,
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF12931	Sec16_C	445 → 715	Sec23-binding domain of Sec16	Domain
  PF12932	Sec16	279 → 378	Vesicle coat trafficking protein Sec16 mid-region	Domain

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:12244571, ECO:0000269|PubMed:17192411}.
• Sequence:

  MELWAPQRLPQTRGKATAPSKDPDRGFRRDGHHRPVPHSWHNGERFHQWQDNRGSPQPQQ
  EPRADHQQQPHYASRPGDWHQPVSGVDYYEGGYRNQLYSRPGYENSYQSYQSPTMREEYA
  YGSYYYHGHPQWLQEERVPRQRSPYIWHEDYREQKYLDEHHYENQHSPFGTNSETHFQSN
  SRNPCKDSPASNSGQEWPGELFPGSLLAEAQKNKPSLASESNLLQQRESGLSSSSYELSQ
  YIRDAPERDDPPASAAWSPVQADVSSAGPKAPMKFYIPHVPVSFGPGGQLVHVGPSSPTD
  GQAALVELHSMEVILNDSEEQEEMRSFSGPLIREDVHKVDIMTFCQQKAAQSCKSETLGS
  RDSALLWQLLVLLCRQNGSMVGSDIAELLMQDCKKLEKYKRQPPVANLINLTDEDWPVLS
  SGTPNLLTGEIPPSVETPAQIVEKFTRLLYYGRKKEALEWAMKNHLWGHALFLSSKMDPQ
  TYSWVMSGFTSTLALNDPLQTLFQLMSGRIPQAATCCGEKQWGDWRPHLAVILSNQAGDP
  ELYQRAIVAIGDTLAGKGLVEAAHFCYLMAHVPFGHYTVKTDHLVLLGSSHSQEFLKFAT
  TEAIQRTEIFEYCQMLGRPKSFIPSFQVYKLLYASRLADYGLVSQALHYCEAIGAAVLSQ
  GESSHPVLLVELIKLAEKLKLSDPLVLERRSGDRDLEPDWLAQLRRQLEQKVAGDIGDPH
  PTRSDISGAGGTTTENTFYQDFSGCQGYSEAPGYRSALWLTPEQTCLLQPSPQQPFPLQP
  GSYPAGGGAGQTGTPRPFYSVPETHLPGTGSSVAVTEATGGTVWEEMLQTHLGPGENTVS
  QETSQPPDGQEVISKPQTPLAARPRSISESSASSAKEDEKESSDEADKNSPRNTAQRGKL
  GDGKEHTKSSGFGWFSWFRSKPTKNASPAGDEDSSDSPDSEETPRASSPHQAGLGLSLTP
  SPESPPLPDVSAFSRGRGGGEGRGSASSGGAAAGAGVGGLSGPESVSFELCSNPGVLLPP
  PALKGAVPLYNPSQVPQLPTATSLNRPNRLAQRRYPTQPC

• Sequence length: 1060

Pathways

Reactome Pathway:

COPII-mediated vesicle transport

Associated diseases

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)

Unknown / Other Associations Show/Hide Unknown Diseases (26)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AMYOTROPHIC LATERAL SCLEROSIS	—	GWAS catalog	22959728	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	36137488	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BODY WEIGHT	—	CTD	22344219, 22344221	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BONE FRAGILITY WITH CONTRACTURES, ARTERIAL RUPTURE, AND DEAFNESS	—	CTD	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CANCER	—	GWAS catalog	29059683	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	29059683	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	37359372	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	39406924	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	31589552, 39349817	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MORBID OBESITY	—	GWAS catalog	39024449	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	23563607, 30677029, 31504550, 36137488, 39024449	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, HIP	—	GWAS catalog	40205036	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	40205036	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS-PSEUDOGLIOMA SYNDROME	—	CTD	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOAFFECTIVE DISORDER	—	GWAS catalog	31591465	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	23894747, 26198764, 28991256, 30285260, 31591465, 35396580	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	31417091	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SLEEP APNEA	—	GWAS catalog	36525587	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	30297969, 31589552, 32499647, 32541925, 34594039, 35551307, 38374256, 38685053, 39349817	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (15)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Breast Carcinoma	Breast Carcinoma	BEFREE	29436922		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Neoplasms	Breast neoplasm	Pubtator	29436922	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	20712903	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	21976109	Associate	★☆☆☆☆ Found in Text Mining only
Glucocorticoid Receptor Deficiency	Glucocorticoid receptor deficiency/resistance	Pubtator	30026463	Associate	★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	36916446	Associate	★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Diabetes mellitus, type 2	Pubtator	32260174	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29436922		★☆☆☆☆ Found in Text Mining only
Niemann-Pick Disease, Type C1	Sphingomyelinase deficiency	BEFREE	19851340		★☆☆☆☆ Found in Text Mining only
NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2A	Night blindness	BEFREE	12552565		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	19851340, 20616199, 21796137, 22041983, 23121087, 24670271, 26800887		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	Pubtator	20616199, 20712903, 21779088, 21796137, 21976109, 23349760, 23408508, 23950976, 26800887, 27421018, 31936053, 33668547, 33801339, 34836030, 36839421, 37709841	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	GWASDB_DG	22484627		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Osteogenesis Imperfecta	Osteogenesis imperfecta	Pubtator	36916446	Associate	★☆☆☆☆ Found in Text Mining only
Spondylocostal dysostosis autosomal recessive	Spondylocostal dysostosis	Pubtator	36916446	Associate	★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

P4HA1 2 shared diseasesBone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome 2 shared evidence sourcesCTD (Bone fragility with contractures, arterial rupture, and deafness), CTD (Osteoporosis-pseudoglioma syndrome) Related via 2 shared diseases including Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome — evidence mostly CTD. MESD 2 shared diseasesBone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome 2 shared evidence sourcesCTD (Bone fragility with contractures, arterial rupture, and deafness), CTD (Osteoporosis-pseudoglioma syndrome) Related via 2 shared diseases including Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome — evidence mostly CTD. P3H1 2 shared diseasesBone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome 2 shared evidence sourcesCTD (Bone fragility with contractures, arterial rupture, and deafness), CTD (Osteoporosis-pseudoglioma syndrome) Related via 2 shared diseases including Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome — evidence mostly CTD. PPIB 2 shared diseasesBone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome 2 shared evidence sourcesCTD (Bone fragility with contractures, arterial rupture, and deafness), CTD (Osteoporosis-pseudoglioma syndrome) Related via 2 shared diseases including Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome — evidence mostly CTD. SGMS2 2 shared diseasesBone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome 2 shared evidence sourcesCTD (Bone fragility with contractures, arterial rupture, and deafness), CTD (Osteoporosis-pseudoglioma syndrome) Related via 2 shared diseases including Bone fragility with contractures, arterial rupture, and deafness, Osteoporosis-pseudoglioma syndrome — evidence mostly CTD.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
P4HA1	2	["Bone fragility with contractures, arterial rupture, and deafness","Osteoporosis-pseudoglioma syndrome"]	0	[]	2	["CTD (Bone fragility with contractures, arterial rupture, and deafness)","CTD (Osteoporosis-pseudoglioma syndrome)"]
MESD	2	["Bone fragility with contractures, arterial rupture, and deafness","Osteoporosis-pseudoglioma syndrome"]	0	[]	2	["CTD (Bone fragility with contractures, arterial rupture, and deafness)","CTD (Osteoporosis-pseudoglioma syndrome)"]
P3H1	2	["Bone fragility with contractures, arterial rupture, and deafness","Osteoporosis-pseudoglioma syndrome"]	0	[]	2	["CTD (Bone fragility with contractures, arterial rupture, and deafness)","CTD (Osteoporosis-pseudoglioma syndrome)"]
PPIB	2	["Bone fragility with contractures, arterial rupture, and deafness","Osteoporosis-pseudoglioma syndrome"]	0	[]	2	["CTD (Bone fragility with contractures, arterial rupture, and deafness)","CTD (Osteoporosis-pseudoglioma syndrome)"]
SGMS2	2	["Bone fragility with contractures, arterial rupture, and deafness","Osteoporosis-pseudoglioma syndrome"]	0	[]	2	["CTD (Bone fragility with contractures, arterial rupture, and deafness)","CTD (Osteoporosis-pseudoglioma syndrome)"]

Diseases Linked via Similar Genes

Desbuquois syndrome Linked via 4 of 5 related genesMESD, P3H1, PPIB, SGMS2 Osteogenesis imperfecta Linked via 3 of 5 related genesMESD, P3H1, PPIB Atrial fibrillation Linked via 1 of 5 related genesP4HA1 Larsen syndrome Linked via 1 of 5 related genesP4HA1 Calvarial doughnut lesions with bone fragility Linked via 1 of 5 related genesSGMS2

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Desbuquois syndrome	4	["MESD","P3H1","PPIB","SGMS2"]
Osteogenesis imperfecta	3	["MESD","P3H1","PPIB"]
Atrial fibrillation	1	["P4HA1"]
Larsen syndrome	1	["P4HA1"]
Calvarial doughnut lesions with bone fragility	1	["SGMS2"]