AVPR2 p.Leu316fs
c.946del · VCV4953428
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
AVPR2-related disorder
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 | escapes | premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.7 | GERP 0.79, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- AVPR2
- Protein
- p.Leu316fs
- Coding
- c.946del
- MANE Select
- NM_000054
- Type
- Deletion
- Location
- chrX:153906557 (GRCh38)
- Structure
- AlphaFold pLDDT 76.84 · 44 PDB
Disease context
AVPR2-related disorder
Similar variants
- AVPR2 p.Ala210fs Likely pathogenic ★ same condition
- AVPR2 p.Gln291fs Likely pathogenic ★ same condition
- AVPR2 p.Leu16fs Pathogenic ★ same condition
- AVPR2 p.Trp193fs Likely pathogenic ★ same condition
- AVPR2 p.Leu316Arg Uncertain significance ★ ⚠ same residue
- AVPR2 p.Leu316= Likely benign ★ same residue
- AVPR2 p.Arg104Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- AVPR2 p.Arg113Trp 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-leu316fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown