AVPR2 p.Pro159fs
c.474del · VCV3598170
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
diabetes insipidus, nephrogenic, X-linked
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 4 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 0.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- AVPR2
- Protein
- p.Pro159fs
- Coding
- c.474del
- MANE Select
- NM_000054
- Type
- Deletion
- Location
- chrX:153905979 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
- Residue 159
- an α-helix; a disulfide bond
Disease context
diabetes insipidus, nephrogenic, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: nephrogenic syndrome of inappropriate antidiuresis
For Arginine vasopressin resistance (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- AVPR2 p.Arg247fs Pathogenic ★★ same condition
- AVPR2 p.Arg251fs Likely pathogenic ★★ same condition
- AVPR2 p.Ile46fs Pathogenic ★★ same condition
- AVPR2 p.Tyr128del Pathogenic/Likely pathogenic ★★ same condition
- AVPR2 p.Tyr205fs Pathogenic ★★ same condition
- AVPR2 p.Ala114_Val115insTer Pathogenic ★ same condition
- AVPR2 p.Glu198fs Pathogenic ★ same condition
- AVPR2 p.Gly69fs Likely pathogenic ★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/avpr2-p-pro159fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown