Is AVPR2 p.Ser255fs (c.763del) pathogenic?

AVPR2 p.Ser255fs (c.763del) is classified Pathogenic in AVPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-19). Absent from gnomAD.

How common is AVPR2 p.Ser255fs (c.763del) in the general population?

AVPR2 p.Ser255fs (c.763del) is absent from gnomAD (gnomAD).

AVPR2 p.Ser255fs

c.763del · rs2521158880 · VCV2737429

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 -1.3	GERP -3.4

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AVPR2
Protein: p.Ser255fs
Coding: c.763del
MANE Select: NM_000054
dbSNP: rs2521158880
Type: Deletion
Location: chrX:153906269 (GRCh38)
Structure: AlphaFold pLDDT 76.84 · 44 PDB
Residue 255: the 'disordered' region

Full AVPR2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AVPR2 p.Arg158fs Pathogenic/Likely pathogenic ★★ same type
AVPR2 p.Arg247fs Pathogenic ★★ same type
AVPR2 p.Arg251fs Likely pathogenic ★★ same type
AVPR2 p.Gly185fs Pathogenic/Likely pathogenic ★★ same type
AVPR2 p.Gly257fs Likely pathogenic ★★ same type
AVPR2 p.Ile46fs Pathogenic ★★ same type
AVPR2 p.Phe328fs Pathogenic/Likely pathogenic ★★ same type
AVPR2 p.Tyr128del Pathogenic/Likely pathogenic ★★ same type

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-ser255fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown