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	84522
Gene name	Jagunal vesicle mediated transporter 1
Gene symbol	JAGN1
Synonyms (NCBI Gene)	GL009SCN6
Chromosome	3
Chromosome location	3p25.3
Summary	The protein encoded by this gene is a transmembrane protein. It functions in the early secretory pathway and is necessary for neutrophil differentiation and survival. Mutations in this gene result in severe congenital neutropenia. [provided by RefSeq, Oct

Show/Hide all (8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs587777727	G>A	Pathogenic	5 prime UTR variant, missense variant, initiator codon variant
rs587777728	C>T	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs587777729	G>T	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs587777730	A>G	Pathogenic	Missense variant, coding sequence variant
rs587777731	CCGACGGCA>-	Pathogenic	5 prime UTR variant, coding sequence variant, inframe deletion
rs777966677	G>A	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs786205704	G>A,T	Pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant
rs786205705	C>G	Pathogenic	Stop gained, coding sequence variant

148

Show/Hide all (148)

miRTarBase ID	miRNA	Experiments	Reference
MIRT648137	hsa-miR-34b-3p	HITS-CLIP	23824327
MIRT648136	hsa-miR-1266-3p	HITS-CLIP	23824327
MIRT648135	hsa-miR-6734-3p	HITS-CLIP	23824327
MIRT648134	hsa-miR-3667-3p	HITS-CLIP	23824327
MIRT648133	hsa-miR-6515-3p	HITS-CLIP	23824327
MIRT648132	hsa-miR-1236-3p	HITS-CLIP	23824327
MIRT648131	hsa-miR-6868-3p	HITS-CLIP	23824327
MIRT648130	hsa-miR-7152-5p	HITS-CLIP	23824327
MIRT648137	hsa-miR-34b-3p	HITS-CLIP	23824327
MIRT648136	hsa-miR-1266-3p	HITS-CLIP	23824327
MIRT648135	hsa-miR-6734-3p	HITS-CLIP	23824327
MIRT648134	hsa-miR-3667-3p	HITS-CLIP	23824327
MIRT648133	hsa-miR-6515-3p	HITS-CLIP	23824327
MIRT648132	hsa-miR-1236-3p	HITS-CLIP	23824327
MIRT648131	hsa-miR-6868-3p	HITS-CLIP	23824327
MIRT648130	hsa-miR-7152-5p	HITS-CLIP	23824327
MIRT1075990	hsa-miR-1193	CLIP-seq
MIRT1075991	hsa-miR-1200	CLIP-seq
MIRT1075992	hsa-miR-143	CLIP-seq
MIRT1075993	hsa-miR-192	CLIP-seq
MIRT1075994	hsa-miR-215	CLIP-seq
MIRT1075995	hsa-miR-23a	CLIP-seq
MIRT1075996	hsa-miR-23b	CLIP-seq
MIRT1075997	hsa-miR-23c	CLIP-seq
MIRT1075998	hsa-miR-3074-5p	CLIP-seq
MIRT1075999	hsa-miR-3150a-3p	CLIP-seq
MIRT1076000	hsa-miR-3175	CLIP-seq
MIRT1076001	hsa-miR-3688-3p	CLIP-seq
MIRT1076002	hsa-miR-452	CLIP-seq
MIRT1076003	hsa-miR-4676-3p	CLIP-seq
MIRT1076004	hsa-miR-4717-3p	CLIP-seq
MIRT1076005	hsa-miR-4770	CLIP-seq
MIRT1076006	hsa-miR-939	CLIP-seq
MIRT1075992	hsa-miR-143	CLIP-seq
MIRT1075993	hsa-miR-192	CLIP-seq
MIRT1075994	hsa-miR-215	CLIP-seq
MIRT2018881	hsa-miR-28-5p	CLIP-seq
MIRT2018882	hsa-miR-3139	CLIP-seq
MIRT2018883	hsa-miR-3180-5p	CLIP-seq
MIRT2018884	hsa-miR-3936	CLIP-seq
MIRT2018885	hsa-miR-4464	CLIP-seq
MIRT2018886	hsa-miR-4474-5p	CLIP-seq
MIRT2018887	hsa-miR-4748	CLIP-seq
MIRT1076005	hsa-miR-4770	CLIP-seq
MIRT2018888	hsa-miR-513c	CLIP-seq
MIRT2018889	hsa-miR-514b-5p	CLIP-seq
MIRT2018890	hsa-miR-520a-5p	CLIP-seq
MIRT2018891	hsa-miR-525-5p	CLIP-seq
MIRT2018892	hsa-miR-708	CLIP-seq
MIRT2018881	hsa-miR-28-5p	CLIP-seq
MIRT2250758	hsa-miR-3130-5p	CLIP-seq
MIRT2018882	hsa-miR-3139	CLIP-seq
MIRT2250759	hsa-miR-3168	CLIP-seq
MIRT2250760	hsa-miR-4277	CLIP-seq
MIRT2018885	hsa-miR-4464	CLIP-seq
MIRT2250761	hsa-miR-4482	CLIP-seq
MIRT2250762	hsa-miR-4662a-5p	CLIP-seq
MIRT2018887	hsa-miR-4748	CLIP-seq
MIRT2018888	hsa-miR-513c	CLIP-seq
MIRT2018889	hsa-miR-514b-5p	CLIP-seq
MIRT2018892	hsa-miR-708	CLIP-seq
MIRT2018881	hsa-miR-28-5p	CLIP-seq
MIRT2389539	hsa-miR-3130-3p	CLIP-seq
MIRT2018882	hsa-miR-3139	CLIP-seq
MIRT2018883	hsa-miR-3180-5p	CLIP-seq
MIRT2389540	hsa-miR-3663-5p	CLIP-seq
MIRT2389541	hsa-miR-4527	CLIP-seq
MIRT2389542	hsa-miR-4733-3p	CLIP-seq
MIRT2389543	hsa-miR-4793-3p	CLIP-seq
MIRT2018890	hsa-miR-520a-5p	CLIP-seq
MIRT2018891	hsa-miR-525-5p	CLIP-seq
MIRT2018892	hsa-miR-708	CLIP-seq
MIRT2389544	hsa-miR-767-5p	CLIP-seq
MIRT1075990	hsa-miR-1193	CLIP-seq
MIRT2554199	hsa-miR-1226	CLIP-seq
MIRT1075992	hsa-miR-143	CLIP-seq
MIRT2554200	hsa-miR-186	CLIP-seq
MIRT1075993	hsa-miR-192	CLIP-seq
MIRT2554201	hsa-miR-214	CLIP-seq
MIRT1075994	hsa-miR-215	CLIP-seq
MIRT2018881	hsa-miR-28-5p	CLIP-seq
MIRT2389539	hsa-miR-3130-3p	CLIP-seq
MIRT2554202	hsa-miR-3133	CLIP-seq
MIRT2018882	hsa-miR-3139	CLIP-seq
MIRT1075999	hsa-miR-3150a-3p	CLIP-seq
MIRT1076000	hsa-miR-3175	CLIP-seq
MIRT2018883	hsa-miR-3180-5p	CLIP-seq
MIRT2554203	hsa-miR-3619-5p	CLIP-seq
MIRT2389540	hsa-miR-3663-5p	CLIP-seq
MIRT1076001	hsa-miR-3688-3p	CLIP-seq
MIRT2018884	hsa-miR-3936	CLIP-seq
MIRT2554204	hsa-miR-3938	CLIP-seq
MIRT2554205	hsa-miR-4291	CLIP-seq
MIRT2554206	hsa-miR-4470	CLIP-seq
MIRT2018886	hsa-miR-4474-5p	CLIP-seq
MIRT2389541	hsa-miR-4527	CLIP-seq
MIRT2554207	hsa-miR-4668-3p	CLIP-seq
MIRT2554208	hsa-miR-4715-3p	CLIP-seq
MIRT2389542	hsa-miR-4733-3p	CLIP-seq
MIRT1076005	hsa-miR-4770	CLIP-seq
MIRT2389543	hsa-miR-4793-3p	CLIP-seq
MIRT2554209	hsa-miR-499-3p	CLIP-seq
MIRT2554210	hsa-miR-499a-3p	CLIP-seq
MIRT2018890	hsa-miR-520a-5p	CLIP-seq
MIRT2018891	hsa-miR-525-5p	CLIP-seq
MIRT2554211	hsa-miR-548ac	CLIP-seq
MIRT2554212	hsa-miR-548d-3p	CLIP-seq
MIRT2554213	hsa-miR-548z	CLIP-seq
MIRT2018892	hsa-miR-708	CLIP-seq
MIRT2554214	hsa-miR-761	CLIP-seq
MIRT2389544	hsa-miR-767-5p	CLIP-seq
MIRT2554215	hsa-miR-922	CLIP-seq
MIRT1076006	hsa-miR-939	CLIP-seq
MIRT1075990	hsa-miR-1193	CLIP-seq
MIRT1075992	hsa-miR-143	CLIP-seq
MIRT2554200	hsa-miR-186	CLIP-seq
MIRT1075993	hsa-miR-192	CLIP-seq
MIRT2554201	hsa-miR-214	CLIP-seq
MIRT1075994	hsa-miR-215	CLIP-seq
MIRT2018881	hsa-miR-28-5p	CLIP-seq
MIRT2389539	hsa-miR-3130-3p	CLIP-seq
MIRT2554202	hsa-miR-3133	CLIP-seq
MIRT2018882	hsa-miR-3139	CLIP-seq
MIRT1075999	hsa-miR-3150a-3p	CLIP-seq
MIRT1076000	hsa-miR-3175	CLIP-seq
MIRT2018883	hsa-miR-3180-5p	CLIP-seq
MIRT2554203	hsa-miR-3619-5p	CLIP-seq
MIRT2389540	hsa-miR-3663-5p	CLIP-seq
MIRT1076001	hsa-miR-3688-3p	CLIP-seq
MIRT2018884	hsa-miR-3936	CLIP-seq
MIRT2554204	hsa-miR-3938	CLIP-seq
MIRT2554205	hsa-miR-4291	CLIP-seq
MIRT2554206	hsa-miR-4470	CLIP-seq
MIRT2018886	hsa-miR-4474-5p	CLIP-seq
MIRT2389541	hsa-miR-4527	CLIP-seq
MIRT2554208	hsa-miR-4715-3p	CLIP-seq
MIRT2389542	hsa-miR-4733-3p	CLIP-seq
MIRT1076005	hsa-miR-4770	CLIP-seq
MIRT2389543	hsa-miR-4793-3p	CLIP-seq
MIRT2554209	hsa-miR-499-3p	CLIP-seq
MIRT2554210	hsa-miR-499a-3p	CLIP-seq
MIRT2018890	hsa-miR-520a-5p	CLIP-seq
MIRT2018891	hsa-miR-525-5p	CLIP-seq
MIRT2018892	hsa-miR-708	CLIP-seq
MIRT2554214	hsa-miR-761	CLIP-seq
MIRT2389544	hsa-miR-767-5p	CLIP-seq
MIRT2554215	hsa-miR-922	CLIP-seq
MIRT1076006	hsa-miR-939	CLIP-seq

Show/Hide all (25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002376	Process	Immune system process	IEA
GO:0002446	Process	Neutrophil mediated immunity	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 32296183
GO:0005783	Component	Endoplasmic reticulum	IDA	25129144
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0006887	Process	Exocytosis	TAS	25129144
GO:0007029	Process	Endoplasmic reticulum organization	IBA
GO:0007029	Process	Endoplasmic reticulum organization	IEA
GO:0009749	Process	Response to glucose	IEA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IBA
GO:0016192	Process	Vesicle-mediated transport	IMP	25129144
GO:0030073	Process	Insulin secretion	IEA
GO:0030223	Process	Neutrophil differentiation	IMP	25129144
GO:0034976	Process	Response to endoplasmic reticulum stress	IEA
GO:0038158	Process	Granulocyte colony-stimulating factor signaling pathway	IBA
GO:0038158	Process	Granulocyte colony-stimulating factor signaling pathway	IEA
GO:0038158	Process	Granulocyte colony-stimulating factor signaling pathway	IMP	25129144
GO:0050832	Process	Defense response to fungus	IEA
GO:0061179	Process	Negative regulation of insulin secretion involved in cellular response to glucose stimulus	IEA
GO:1901142	Process	Insulin metabolic process	IEA
GO:1990266	Process	Neutrophil migration	IEA

MIM	HGNC	e!Ensembl
616012	26926	ENSG00000171135

Q8N5M9

Protein name

Protein jagunal homolog 1

Protein function

Endoplasmic reticulum transmembrane protein involved in vesicle-mediated transport, which is required for neutrophil function. Required for vesicle-mediated transport; it is however unclear whether it is involved in early secretory pathway or in

PDB

6WVD

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF07086	Jagunal	1 → 177	Jagunal, ER re-organisation during oogenesis	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:25129144}.

Sequence

MASRAGPRAAGTDGSDFQHRERVAMHYQMSVTLKYEIKKLIYVHLVIWLLLVAKMSVGHL
RLLSHDQVAMPYQWEYPYLLSILPSLLGLLSFPRNNISYLVLSMISMGLFSIAPLIYGSM
EMFPAAQQLYRHGKAYRFLFGFSAVSIMYLVLVLAVQVHAWQLYYSKKLLDSWFTSTQEK
KHK

Sequence length

183

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
Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency	Pathogenic	rs587777730	RCV000144165	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe congenital neutropenia	Pathogenic	rs587777730, rs786205705	RCV000170605 RCV000170604	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (5)

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.
JAGN1-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA, SEVERE CONGENITAL, 6, AUTOSOMAL RECESSIVE	—	CTD, HPO CTD, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE CONGENITAL NEUTROPENIA DUE TO JAGN1 DEFICIENCY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE CONGENITAL NEUTROPENIA TYPE 6, AUTOSOMAL RECESSIVE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (15)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency	Congenital Neutropenia	Orphanet			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital neutropenia	Congenital Neutropenia	BEFREE	25129144, 25851723, 30028820, 30044346, 30106500		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital neutropenia	Congenital Neutropenia	GENOMICS_ENGLAND_DG	25129144		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukopenia	Leukopenia	BEFREE	30044346		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neutropenia	Neutropenia	CTD_human_DG	25129144, 25129145		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neutropenia	Neutropenia	BEFREE	30044346		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neutropenia	Neutropenia	Pubtator	39286252	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neutropenia	Neutropenia	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Neutropenia Severe Congenital Autosomal Recessive 3	Severe congenital neutropenia	Pubtator	25129144, 30040071, 32419428, 33206996, 39286252	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
NEUTROPENIA, SEVERE CONGENITAL, 6, AUTOSOMAL RECESSIVE	Neutropenia	GENOMICS_ENGLAND_DG	11101832, 25129144		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA, SEVERE CONGENITAL, 6, AUTOSOMAL RECESSIVE	Neutropenia	UNIPROT_DG	25129144		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA, SEVERE CONGENITAL, 6, AUTOSOMAL RECESSIVE	Neutropenia	ORPHANET_DG	25129144		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA, SEVERE CONGENITAL, 6, AUTOSOMAL RECESSIVE	Neutropenia	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA, SEVERE CONGENITAL, 6, AUTOSOMAL RECESSIVE	Neutropenia	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Recurrent otitis media	Otitis media	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

JAGN1 (jagunal vesicle mediated transporter 1)