Is AVPR2 p.Trp193fs (c.579_580del) pathogenic?

AVPR2 p.Trp193fs (c.579580del) is classified Likely pathogenic in AVPR2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-17). Absent from gnomAD; Associated with AVPR2-related disorder.

What condition is associated with AVPR2 p.Trp193fs (c.579_580del)?

AVPR2 p.Trp193fs (c.579_580del) is associated with AVPR2-related disorder (ClinVar).

How common is AVPR2 p.Trp193fs (c.579_580del) in the general population?

AVPR2 p.Trp193fs (c.579_580del) is absent from gnomAD (gnomAD).

AVPR2 p.Trp193fs

c.579_580del · rs2521156768 · VCV2629646

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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	predicted	premature termination codon in exon 3 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1

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.Trp193fs
Coding: c.579_580del
MANE Select: NM_000054
dbSNP: rs2521156768
Type: Deletion
Location: chrX:153906084 (GRCh38)
Structure: AlphaFold pLDDT 76.84 · 44 PDB
Residue 193: a β-strand

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

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.Leu316fs Likely pathogenic ★ same condition
AVPR2 p.Trp193Ter Pathogenic ★ same residue
AVPR2 p.Arg104Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
AVPR2 p.Arg113Trp Pathogenic ★★ same condition
AVPR2 p.Arg137His 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-trp193fs (accessed [today's date]).

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