JAGN1

Chr 3AR

jagunal vesicle mediated transporter 1

Also known as: GL009, SCN6

NCBI Gene: 84522ENSG00000171135UniProt: Q8N5M9OMIM: 616012

This endoplasmic reticulum transmembrane protein regulates vesicle-mediated transport and is essential for neutrophil differentiation, survival, and function including defense against fungal pathogens. Mutations cause severe congenital neutropenia with autosomal recessive inheritance, typically presenting in the neonatal period with recurrent infections.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.351 OMIM phenotype
Clinical Summary— JAGN1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
51 unique Pathogenic / Likely Pathogenic· 110 VUS of 240 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.35LOEUF
pLI 0.007
Z-score 0.97
OE 0.60 (0.29–1.35)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.06Z-score
OE missense 0.98 (0.84–1.16)
103 obs / 104.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.60 (0.29–1.35)
0≤0.351.4
Missense OE0.98 (0.84–1.16)
0≤0.61.4
Synonymous OE1.17
0≤1.21.6
LoF obs/exp: 4 / 6.7Missense obs/exp: 103 / 104.7Syn Z: -0.84
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveJAGN1-related severe congenital neutropeniaLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6841th %ile
GOF
0.6442th %ile
LOF
0.2679th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

240 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic46
Likely Pathogenic5
VUS110
Likely Benign57
Benign11
Conflicting8
46
Pathogenic
5
Likely Pathogenic
110
VUS
57
Likely Benign
11
Benign
8
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
1
44
0
46
Likely Pathogenic
2
0
3
0
5
VUS
7
77
26
0
110
Likely Benign
0
3
13
41
57
Benign
0
0
8
3
11
Conflicting
—8
Total10819444237

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

JAGN1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients