Phenopacket Example — Netherton Syndrome
Overview
This page presents a Phenopacket v2.0.2 describing a male infant with
OMIM:256500 — Netherton syndrome, caused by a pathogenic variant in SPINK5.
Show raw Phenopacket JSON
{
"id": "PMID_11952552_patient",
"subject": {
"id": "patient",
"timeAtLastEncounter": {
"age": {
"iso8601duration": "P4M"
}
},
"vitalStatus": {
"status": "DECEASED"
},
"sex": "MALE"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0012472",
"label": "Eclabion"
},
"excluded": true
},
{
"type": {
"id": "HP:0000656",
"label": "Ectropion"
},
"excluded": true
},
{
"type": {
"id": "HP:0001019",
"label": "Erythroderma"
},
"onset": {
"ontologyClass": {
"id": "HP:0003577",
"label": "Congenital onset"
}
}
},
{
"type": {
"id": "HP:0025092",
"label": "Epidermal acanthosis"
}
},
{
"type": {
"id": "HP:0040190",
"label": "White scaling skin"
},
"onset": {
"ontologyClass": {
"id": "HP:0003577",
"label": "Congenital onset"
}
}
},
{
"type": {
"id": "HP:0010783",
"label": "Erythema"
}
},
{
"type": {
"id": "HP:0003777",
"label": "Pili torti"
}
}
],
"interpretations": [
{
"id": "7FevHw7ZYG6vwkStfPR4LfVa",
"progressStatus": "SOLVED",
"diagnosis": {
"disease": {
"id": "OMIM:256500",
"label": "Netherton syndrome"
},
"genomicInterpretations": [
{
"subjectOrBiosampleId": "patient",
"interpretationStatus": "CAUSATIVE",
"variantInterpretation": {
"acmgPathogenicityClassification": "PATHOGENIC",
"therapeuticActionability": "UNKNOWN_ACTIONABILITY",
"variationDescriptor": {
"id": "c153del_SPINK5_NM_006846v4",
"geneContext": {
"valueId": "HGNC:15464",
"symbol": "SPINK5"
},
"expressions": [
{
"syntax": "hgvs.c",
"value": "NM_006846.4:c.153del"
},
{
"syntax": "hgvs.g",
"value": "NC_000005.10:g.148070394del"
},
{
"syntax": "hgvs.p",
"value": "NP_006837.2:p.(Gln52LysfsTer6)"
}
],
"vcfRecord": {
"genomeAssembly": "hg38",
"chrom": "chr5",
"pos": 148070388,
"ref": "AT",
"alt": "A"
},
"moleculeContext": "genomic",
"allelicState": {
"id": "GENO:0000136",
"label": "homozygous"
}
}
}
}
]
}
}
],
"diseases": [
{
"term": {
"id": "OMIM:256500",
"label": "Netherton syndrome"
},
"onset": {
"ontologyClass": {
"id": "HP:0003577",
"label": "Congenital onset"
}
}
}
],
"metaData": {
"created": "2025-12-31T15:52:33.505831Z",
"createdBy": "0000-0002-0736-9199",
"resources": [
{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2025-11-24",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
},
{
"id": "geno",
"name": "Genotype Ontology",
"url": "http://purl.obolibrary.org/obo/geno.owl",
"version": "2025-07-25",
"namespacePrefix": "GENO",
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
},
{
"id": "so",
"name": "Sequence types and features ontology",
"url": "http://purl.obolibrary.org/obo/so.owl",
"version": "2024-11-18",
"namespacePrefix": "SO",
"iriPrefix": "http://purl.obolibrary.org/obo/SO_"
},
{
"id": "omim",
"name": "An Online Catalog of Human Genes and Genetic Disorders",
"url": "https://www.omim.org",
"version": "06/01/25",
"namespacePrefix": "OMIM",
"iriPrefix": "https://www.omim.org/entry/"
},
{
"id": "hgnc",
"name": "HUGO Gene Nomenclature Committee",
"url": "https://www.genenames.org",
"version": "06/01/25",
"namespacePrefix": "HGNC",
"iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
}
],
"phenopacketSchemaVersion": "2.0.2",
"externalReferences": [
{
"id": "PMID:11952552",
"description": "Genetic analysis of a severe case of Netherton syndrome and application for prenatal testing"
}
]
}
}
🧬 Patient Summary
| Field | Value |
|---|---|
| Patient ID | PMID_11952552_patient |
| Sex | Male |
| Age at last encounter | 4 months |
| Vital status | Deceased |
| Primary diagnosis | OMIM:256500 — Netherton syndrome |
| Gene | SPINK5 |
| Variant | NM_006846.4:c.153del |
Clinical context
Netherton syndrome is an autosomal recessive disorder characterized by congenital erythroderma, ichthyosis, and hair shaft abnormalities such as pili torti.
🧾 Phenotypic Features
| HPO ID | Label | Onset |
|---|---|---|
HP:0001019 | Erythroderma | Congenital |
HP:0025092 | Epidermal acanthosis | — |
HP:0040190 | White scaling skin | Congenital |
HP:0010783 | Erythema | — |
HP:0003777 | Pili torti | — |
Tip
Observed features contribute positively to phenotype-driven diagnostics.
| HPO ID | Label |
|---|---|
HP:0012472 | Eclabion |
HP:0000656 | Ectropion |
Why exclusions matter
Explicitly excluded phenotypes help narrow differential diagnoses and improve computational ranking algorithms.
🧬 Genetic Interpretation
Causative Variant Identified
Gene: HGNC:15464 — SPINK5
Allelic state: Homozygous
ACMG classification: Pathogenic
Interpretation status: Causative
Variant Expressions
| Syntax | Value |
|---|---|
| hgvs.c | NM_006846.4:c.153del |
| hgvs.g | NC_000005.10:g.148070394del |
| hgvs.p | NP_006837.2:p.(Gln52LysfsTer6) |
VCF Representation
| Assembly | Chrom | Pos | Ref | Alt |
|---|---|---|---|---|
| hg38 | chr5 | 148070388 | AT | A |
Interpretation
This frameshift deletion leads to premature truncation of the SPINK5 protein, consistent with loss-of-function variants reported in Netherton syndrome.
🧾 Disease
| Field | Value |
|---|---|
| Disease | OMIM:256500 — Netherton syndrome |
| Onset | Congenital onset |
📚 Metadata
| Field | Value |
|---|---|
| Schema Version | 2.0.2 |
| Created | 2025-12-31 |
| External Reference | PMID:11952552 |
Ontology Resources
- Human Phenotype Ontology (HP)
- Genotype Ontology (GENO)
- Sequence Ontology (SO)
- OMIM
- HGNC
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