Is AVPR2 p.Pro322Leu (c.965C>T) pathogenic?

AVPR2 p.Pro322Leu (c.965C>T) is classified Pathogenic/Likely pathogenic in AVPR2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-02-04). AlphaMissense: likely pathogenic (0.9557); Absent from gnomAD v4.1; Associated with nephrogenic diabetes insipidus.

What condition is associated with AVPR2 p.Pro322Leu (c.965C>T)?

AVPR2 p.Pro322Leu (c.965C>T) is associated with nephrogenic diabetes insipidus (ClinVar).

How common is AVPR2 p.Pro322Leu (c.965C>T) in the general population?

AVPR2 p.Pro322Leu (c.965C>T) is absent from gnomAD v4.1 (gnomAD).

How is Arginine vasopressin resistance inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about AVPR2 p.Pro322Leu (c.965C>T)?

AlphaMissense predicts likely pathogenic (score 0.9557) — an in-silico prediction, not a clinical call.

AVPR2 p.Pro322Leu

c.965C>T · rs2521161799 · VCV2138782

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.9557 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

nephrogenic diabetes insipidus

Computational evidence

Protein change
AlphaMissense	0.9557	likely pathogenic ✓ concordant with ClinVar · top 5% in AVPR2
REVEL	0.99	strongly pathogenic-leaning
SaProt	LLR -14.43	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1.9, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 1,579 bp · p 0.00022 · regional, not allelic
Overall
CADD	28.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: AVPR2
Protein: p.Pro322Leu
Coding: c.965C>T
MANE Select: NM_000054
dbSNP: rs2521161799
Type: single nucleotide variant
Location: chrX:153906577 (GRCh38)
Structure: AlphaFold pLDDT 76.84 · 44 PDB
Residue 322: a UniProt-annotated variant site (in ndi1); an α-helix

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

Disease context

nephrogenic diabetes insipidus — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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.Pro322Thr Likely pathogenic ★ same residue
AVPR2 p.Pro322Ser Pathogenic ★ same residue
AVPR2 p.Pro322= Likely benign ★ same residue
AVPR2 p.Arg104Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
AVPR2 p.Arg137His Pathogenic ★★ same condition
AVPR2 p.Tyr205Cys Pathogenic/Likely pathogenic ★★ same condition
AVPR2 p.Ala285Pro Likely pathogenic ★ same condition
AVPR2 p.Arg137Gly 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-pro322leu (accessed [today's date]).

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