# Phenotypic Variability Associated with Jagunal Homolog 1 (JAGN1) Deficiency Caused by the c.63G>T Variant

**Authors:** Cristina-Loredana Pantea, Mihaela Bataneant, Cristian G. Zimbru, Margit Serban, Maria Puiu, Adela Chirita-Emandi

PMC · DOI: 10.3390/ijms27041735 · 2026-02-11

## TL;DR

This study examines the varied symptoms and outcomes in patients with JAGN1 deficiency caused by a specific genetic variant, highlighting differences in clinical presentation and prognosis.

## Contribution

The study provides a detailed clinical characterization of JAGN1 deficiency caused by the c.63G>T variant in Romanian patients and compares it with literature cases.

## Key findings

- Patients with JAGN1 c.63G>T variant showed a wide range of symptoms, including neutropenia and infections.
- Most patients had a homozygous variant and consanguineous background, with a favorable prognosis in Romanian cases.
- No malignancy or leukemia was observed in patients during the follow-up period.

## Abstract

More than 30 distinct genetic entities associated with severe congenital neutropenia (SCN) have been described. SCN has a risk of clonal expansion of mutated hematopoietic cells. Jagunal homolog 1 (JAGN1) deficiency has been described as a genetic cause of SCN and is now estimated to account for approximately 10% of all SCN cases. One prevalent variant in patients with JAGN1 deficiency is NM_032492.4:c.63G>T (p.Glu21Asp). The clinical description and disease evolution study of Romanian patients with JAGN1 deficiency caused by the JAGN1 c.63G>T variant were performed together with a literature review of similar cases. The clinical characterization of six Romanian patients and nine additional patients reported in the literature with JAGN1 deficiency caused by the c.63G>T variant (40% female) revealed a wide phenotypic spectrum, including: neutropenia (all), severe infections (80%), developmental delay (13%), dental problems such as stomatitis/periodontitis (66%), and short stature (7%). No patient developed malignancy/leukemia during the follow-up period (15 ± 8.1 years). Most patients (93%) had a homozygous variant and consanguineous background, while one had compound heterozygous JAGN1 variants. The five Romanian patients carrying this homozygous variant, possibly due to a founder effect, had a relatively favorable clinical outcome, with good overall prognosis.

## Linked entities

- **Genes:** JAGN1 (jagunal vesicle mediated transporter 1) [NCBI Gene 84522]
- **Diseases:** severe congenital neutropenia (MONDO:0018542), neutropenia (MONDO:0001475), stomatitis (MONDO:0004842), periodontitis (MONDO:0005076)

## Full-text entities

- **Genes:** G6PC3 (glucose-6-phosphatase catalytic subunit 3) [NCBI Gene 92579] {aka SCN4, UGRP}, GATA2 (GATA binding protein 2) [NCBI Gene 2624] {aka DCML, IMD21, MONOMAC, NFE1B}, CSF3 (colony stimulating factor 3) [NCBI Gene 1440] {aka C17orf33, CSF3OS, GCSF}, CLPB (ClpB family mitochondrial disaggregase) [NCBI Gene 81570] {aka ANKCLB, ANKCLP, HSP78, MEGCANN, MGCA7, MGCA7A}, CSF3R (colony stimulating factor 3 receptor) [NCBI Gene 1441] {aka CD114, GCSFR, SCN7}, JAGN1 (jagunal vesicle mediated transporter 1) [NCBI Gene 84522] {aka GL009, SCN6}, ELANE (elastase, neutrophil expressed) [NCBI Gene 1991] {aka ELA2, GE, HLE, HNE, NE, PMN-E}, SBDS (SBDS ribosome maturation factor) [NCBI Gene 51119] {aka CGI-97, SDO1, SDS, SWDS}, COPZ1 (coat protein complex I subunit zeta 1) [NCBI Gene 22818] {aka CGI-120, COPZ, HSPC181, SCN12, zeta-COP, zeta1-COP}, GFI1 (growth factor independent 1 transcriptional repressor) [NCBI Gene 2672] {aka GFI-1, GFI1A, SCN2, ZNF163}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, HAX1 (HCLS1 associated protein X-1) [NCBI Gene 10456] {aka HCLSBP1, HS1BP1, SCN3}
- **Diseases:** GATA2 deficiency (MESH:D000077428), AML (MESH:D015470), seizures (MESH:D012640), genetic disorders (MESH:D030342), MDS (MESH:D009190), meningocele (MESH:D008588), hematologic malignancy (MESH:D019337), facial dysmorphic features (MESH:C536503), epistaxis (MESH:D004844), delayed tooth eruption (MESH:D014079), Pneumonia (MESH:D011014), strabismus (MESH:D013285), oral mucosal lesions (MESH:D009059), Hypogammaglobulinemia (MESH:D000361), Bleeding (MESH:D006470), obesity (MESH:D009765), facial dysmorphism (MESH:C565579), X-linked neutropenia (MESH:C564539), JAGN1 deficiency (MESH:D006086), lymphopenia (MESH:D008231), congenital (MESH:D008209), malignancy (MESH:D009369), enamel hypoplasia (MESH:D003744), osteoarticular pain (MESH:D010146), short stature (MESH:D006130), monocytopenia (OMIM:614172), sinusitis (MESH:D012852), injury to (MESH:D014947), Periodontitis (MESH:D010518), inflammation (MESH:D007249), abscesses (MESH:D000038), congenital defects of phagocyte (MESH:D000013), mouth ulcers (MESH:D019226), tooth loss (MESH:D016388), nephrolithiasis (MESH:D053040), aphthous lesions or ulcerations (MESH:D013281), Serum immunoglobulin abnormalities (MESH:D012713), sepsis (MESH:D018805), Chronic Neutropenia (MESH:C535815), infectious (MESH:D003141), hypodontia (MESH:D000848), dental problems (MESH:D019973), autosomal recessive severe congenital neutropenia type 6 (OMIM:616022), tooth (MESH:D014076), Periodontal disease (MESH:D010510), developmental delay (MESH:D002658), hepatitis (MESH:D056486), Hypergammaglobulinemia (MESH:D006942), tuberculosis (MESH:D014376), skeletal malformations (MESH:C535850), chronic gingivitis (MESH:D005891), stomatitis (MESH:D013280), Stilling-Turk-Duane type 1 syndrome (MESH:D004370), neurodevelopmental delay (MESH:D006968), infection (MESH:D007239), thrombocytopenia (MESH:D013921), IEI (MESH:D007154), leukemic transformation (MESH:D002472), Monocytosis (MESH:C538328), hematological abnormalities (MESH:D006402)
- **Species:** Homo sapiens (human, species) [taxon 9606]
- **Mutations:** c.36del, p.Asp13Thrfs*17, c.35_43delCCGACGGCA, p.(Arg361Cys), P21, c.172C>A, p.(Pro58Thr), c.130-131 ins A, c.117_122dup
- **Cell lines:** NM_032492.4 — Bos taurus (Bovine), Finite cell line (CVCL_3074)

## Figures

1 figure with captions in the complete paper: https://tomesphere.com/paper/PMC12940244/full.md

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Source: https://tomesphere.com/paper/PMC12940244