JAGN1 jagunal homolog 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: JAGN1provided by HGNC
Official Full Name: jagunal homolog 1provided by HGNC
Primary source: HGNC:HGNC:26926
See related: Ensembl:ENSG00000171135 MIM:616012; AllianceGenome:HGNC:26926
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SCN6; GL009
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 2014]
Expression: Ubiquitous expression in adrenal (RPKM 15.3), liver (RPKM 12.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.3

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (9890610..9894349)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (9882615..9886362)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (9932294..9936033)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

JAGN1 mutation with distinct clinical features; two case reports and literature review.
Title: JAGN1 mutation with distinct clinical features; two case reports and literature review.
A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans.
Title: A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans.
Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.
Title: Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.
JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting?
Title: JAGN1, tetraspanins, and Erv proteins: is common topology indicative of common function in cargo sorting?
JAGN1 regulates neutrophil myeloperoxidase mRNA and protein levels. Myeloperoxidase is required for fungal killing by neutrophil extracellular traps.
Title: JAGN1 is required for fungal killing in neutrophil extracellular traps: Implications for severe congenital neutropenia.
Data directly identify Jagn1 (JAGN1 in humans) as a new regulator of neutrophil function in microbial pathogenesis.
Title: Jagunal homolog 1 is a critical regulator of neutrophil function in fungal host defense.
JAGN1 participates in the secretory pathway and is required for granulocyte colony-stimulating factor receptor-mediated signaling. JAGN1 emerges as a factor that is necessary in the differentiation and survival of neutrophils.
Title: JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency MedGen: C4014954 OMIM: 616022 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in defense response to fungus	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	TAS Traceable Author Statement more info	PubMed
involved_in granulocyte colony-stimulating factor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in granulocyte colony-stimulating factor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of insulin secretion involved in cellular response to glucose stimulus	IEA Inferred from Electronic Annotation more info
involved_in neutrophil differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neutrophil mediated immunity	IEA Inferred from Electronic Annotation more info
involved_in neutrophil migration	IEA Inferred from Electronic Annotation more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protein jagunal homolog 1

NCBI Reference Sequences (RefSeq)

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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.

Genomic

NG_041779.1 RefSeqGene

Range

5024..8763

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1228

mRNA and Protein(s)

NM_001363890.1 → NP_001350819.1 protein jagunal homolog 1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' terminal exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a

Source sequence(s)

AA310892, AW001569, BC008507, BP262753, BU674942

Conserved Domains (1) summary

pfam07086
Location:1 → 120

Jagunal; ER re-organisation during oogenesis
NM_032492.4 → NP_115881.3 protein jagunal homolog 1 isoform a

See identical proteins and their annotated locations for NP_115881.3

Status: REVIEWED

Description

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

Source sequence(s)

BC008507, BP262753, BU674942

Consensus CDS

CCDS2588.1

UniProtKB/Swiss-Prot

Q8N5M9, Q8NCF6, Q96SW1

Related

ENSP00000496942.1, ENST00000647897.1

Conserved Domains (1) summary

pfam07086
Location:1 → 174

Jagunal; Jagunal, ER re-organisation during oogenesis