# Intellectual disorder type 98 caused by a novel NEXMIF variant: a case report and literature review

**Authors:** Yuanhang Zhu, Fangying Cui, Xuezhe Ouyang, Jing Guo, Yaming Liu, Naiqi Li, Qian Yang, Yali Li, Ling Liu

PMC · DOI: 10.3389/fmed.2026.1757682 · Frontiers in Medicine · 2026-02-06

## TL;DR

A new genetic variant in the NEXMIF gene is linked to intellectual disorder type 98, highlighting the importance of genetic testing for early diagnosis and family counseling.

## Contribution

A novel NEXMIF variant is identified, expanding the known mutational spectrum of intellectual disorder type 98.

## Key findings

- A novel hemizygous NEXMIF variant was found in a child with severe intellectual disability.
- Prenatal diagnosis identified the same variant in a male fetus, leading to informed reproductive counseling.
- The case highlights the role of genetic testing in managing X-linked intellectual disorders.

## Abstract

Intellectual disorder, Type 98 (ID 98) is an X-linked disorder characterized by intellectual disability, epilepsy, and multisystem manifestations. This condition is caused by pathogenic variants in the NEXMIF gene through X-linked dominant inheritance.

We identified a novel hemizygous NEXMIF variant (c.1939_1942delinsAT, p.S647Ifs*3) in a 5-year-old male with severe intellectual disability via trio whole-exome sequencing. His mildly affected mother was a heterozygous carrier. Prenatal diagnosis for the mother’s subsequent pregnancy identified the same hemizygous variant in the male fetus. Following genetic counseling, the decision was made to terminate the pregnancy, thereby preventing the clinical manifestation of the disease in the offspring.

This report expands the NEXMIF mutational spectrum and underscores the critical role of genetic testing in achieving early diagnosis and informed reproductive counseling for families affected by this disorder.

## Linked entities

- **Genes:** NEXMIF (neurite extension and migration factor) [NCBI Gene 340533]

## Full-text entities

- **Genes:** TSC2 (TSC complex subunit 2) [NCBI Gene 7249] {aka LAM, PPP1R160, TSC4}, FMR1 (fragile X messenger ribonucleoprotein 1) [NCBI Gene 2332] {aka FMRP, FRAXA, POF, POF1}, NEXMIF (neurite extension and migration factor) [NCBI Gene 340533] {aka KIAA2022, KIDLIA, MRX98, XLID98, XPN}, Dlg4 (discs large MAGUK scaffold protein 4) [NCBI Gene 13385] {aka Dlgh4, PSD-95, PSD95, SAP90, SAP90A}, Cdh2 (cadherin 2) [NCBI Gene 12558] {aka CDHN, N-CAD, Ncad}, Rhoa (ras homolog family member A) [NCBI Gene 11848] {aka Arha, Arha1, Arha2}, Gphn (gephyrin) [NCBI Gene 268566] {aka 5730552E08Rik, C230040D23, GPH, GPHRYN, geph}, TSC1 (TSC complex subunit 1) [NCBI Gene 7248] {aka LAM, TSC}
- **Diseases:** anxiety (MESH:D001007), frontal cortical atrophy (MESH:D001284), MAE-EMA syndrome (OMIM:616421), glucose abnormalities (MESH:D044882), low-set ears (MESH:C537239), X-linked disorder (MESH:D040181), behavioral deficits (MESH:D019958), ASD (MESH:D001321), Torpedo maculopathy (MESH:D008268), keratoconus (MESH:D007640), hypoplastic uterus (MESH:D014594), behavioral abnormalities (MESH:D001523), brain atrophy (MESH:C566985), cardiac rhabdomyoma (MESH:D012207), insomnia (MESH:D007319), clenching (MESH:C537232), nephrotic syndrome (MESH:D009404), Jeavons syndrome (MESH:D013577), growth retardation (MESH:D006130), sleep disturbances (MESH:D012893), cortical visual impairment (MESH:D014786), brachydactyly (MESH:D059327), camptodactyly (MESH:C567780), IUGR (MESH:D005317), atrial septal defect (MESH:D006344), Gastroesophageal reflux disease (MESH:D005764), spasticity (MESH:D009128), oligohydramnios (MESH:D016104), muscular atrophy (MESH:D009133), hypermobility of (MESH:C536196), HGMD (MESH:C579880), vomiting (MESH:D014839), hand movements (MESH:D006230), mitral regurgitation (MESH:D008944), amenorrhea (MESH:D000568), hyperactivity (MESH:D006948), XLID syndromes (MESH:C538258), neurological disorders (MESH:D009461), heel cord tightness (MESH:C536920), hyperreflexia (MESH:D012021), Seizure (MESH:D012640), FXS (MESH:D005600), Type 98 (OMIM:614861), genetic (MESH:D030342), craniofacial dysmorphism (MESH:C537512), drooling (MESH:D012798), fetal abnormalities (MESH:D005315), strabismus (MESH:D013285), dysmotility (MESH:D015154), microcephaly (MESH:D008831), self-injury (MESH:D012652), intellectual impairment (MESH:C565406), kyphosis (MESH:D007738), multiorgan dysfunction syndrome (MESH:D009102), infantile spasms (MESH:D013036), obesity (MESH:D009765), aortic stenosis (MESH:D001024), mood disorders (MESH:D019964), language deficit (MESH:D007806), hypertonia (MESH:D009122)
- **Chemicals:** valproate (MESH:D014635), POP-7 polymer (-), steroid (MESH:D013256)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606], Danio rerio (leopard danio, species) [taxon 7955]
- **Mutations:** p.M295Vfs*2, c.1939_1942delinsAT, p.D1161Y, c.1939_1942delinsAT, p.S882*, p.S647Ifs*3, p.I446L, p.Arg628*, c.1882C>T, p.S747N, p.C967S, p.S677*, p.S647Ifs*3

## Full text

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## Figures

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## References

53 references — full list in the complete paper: https://tomesphere.com/paper/PMC12920596/full.md

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Source: https://tomesphere.com/paper/PMC12920596