Playground
If you don’t have a suitable VCF on hand for testing, we’ve prepared 4 sample datasets to help you get started with Noxia.
All of them are built from a single public sample, NA12878:
- NA12878 (negative control) — common variants with a gnomAD population frequency > 10% have been removed.
- 3 positive cases — the clinical descriptions come from real cases published in the Chinese Journal of Evidence-Based Pediatrics; for each, we inserted the reported pathogenic variant into the NA12878 VCF above to create an analyzable positive sample.
Once downloaded, you can ask Noxia to analyze them in Claude Code. We recommend trying the negative control first, then taking on the 3 positive cases.
Negative control
NA12878
Common variants with a population frequency > 10% have been removed; useful for calibration and as a control.
Positive cases
Case 1: KIF11 gene variant (MCLMR syndrome)
A 7-year-old boy. Proportionate short stature, microcephaly, and dysmorphic facial features (slightly full forehead, ptosis with downward-slanting eyelids, protruding ears); motor development largely normal but delayed cognitive development; fundus examination suggested choroidal and retinal hypoplasia.
Family-based whole-exome sequencing showed the child carried a KIF11 (NM_004523.3:c.1306-1G>A) variant, not carried by the parents or older brother, consistent with autosomal dominant inheritance. Per ACMG guidelines it was classified as a pathogenic variant (PVS1 + PS2_Moderate + PM2). The diagnosis was microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability syndrome (MCLMR, OMIM 152950).
Ma Chunmiao, Chen Junhui, Liu Junfeng, et al. A KIF11 gene variant associated with microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability syndrome: a case report and literature review [J]. Chinese Journal of Evidence-Based Pediatrics, 2026, 21(2): 155-158.
Case 2: SPTAN1 gene variant (hereditary spastic paraplegia type 91)
An 8-year-old boy. Motor milestones largely normal, but since early childhood he walked leaning forward, fell easily, and had a typical waddling gait; examination showed decreased lower-limb muscle strength, hyperactive bilateral biceps/triceps and knee/ankle tendon reflexes, and slightly reduced superficial sensation in the limbs; electromyography suggested a predominantly demyelinating peripheral polyneuropathy.
Genetic testing showed the child carried a heterozygous SPTAN1 (NM_001130438.3:c.77_103dup, p.T34_L35insHHRFKELST) variant; family verification confirmed it as a de novo mutation (both parents wild-type). Per ACMG guidelines it was classified as a likely pathogenic variant (PS2 + PM2_Supporting + PM4).
Zhu Zihao, Hua Ran, Wang Baotian, et al. SPTAN1 gene variant causing hereditary spastic paraplegia type 91: a case report and literature review [J]. Chinese Journal of Evidence-Based Pediatrics, 2026, 21(1): 76-80. DOI: 10.3969/j.issn.1673-5501.2026.01.011
Case 3: NONO gene variant (MRXS34 syndrome)
A 5-day-old boy, transferred to the NICU for “respiratory distress with abdominal distension.” Born premature at 34⁺³ weeks; examination showed a broad forehead, small palpebral fissures, a flat nasal bridge, dysmorphic auricles, bilateral single palmar creases, polydactyly of the right hand, bilateral cryptorchidism, and slightly reduced muscle tone.
Genetic testing showed a heterozygous NONO (NM_001145408.2:c.1093C>T, p.R365*) variant in the Xq13.1 region, located in exon 10 and inherited from the mother, consistent with X-linked recessive inheritance. Per ACMG guidelines it was classified as a pathogenic variant. The diagnosis was X-linked intellectual developmental disorder syndrome type 34 (MRXS34).
Zhang Zichen, Zhu Yuanyuan, Chen Mingyan, et al. NONO gene mutation causing neonatal MRXS34 syndrome: a case report and literature review. Children’s Hospital, Zhejiang University School of Medicine.