Is AVP p.Met1fs (c.3del) pathogenic?

AVP p.Met1fs (c.3del) is classified Pathogenic in AVP (ClinVar, No assertion criteria, 1 submitter; last evaluated 1996-01-01). Absent from gnomAD; Associated with neurohypophyseal diabetes insipidus.

What condition is associated with AVP p.Met1fs (c.3del)?

AVP p.Met1fs (c.3del) is associated with neurohypophyseal diabetes insipidus (ClinVar).

How common is AVP p.Met1fs (c.3del) in the general population?

AVP p.Met1fs (c.3del) is absent from gnomAD (gnomAD).

AVP p.Met1fs

c.3del · rs2148571870 · VCV12210

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurohypophyseal diabetes insipidus

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.4	GERP -0.035, 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: AVP
Protein: p.Met1fs
Coding: c.3del
MANE Select: NM_001243133 · reported on NM_000490
dbSNP: rs2148571870
Type: Deletion
Location: chr20:3084672 (GRCh38)
Structure: AlphaFold pLDDT 81.16 · 27 PDB
Residue 1: the pyrin domain

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

Disease context

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

Similar variants

AVP p.Phe22del Uncertain significance ★ same condition
AVP p.Ser87_Gln89del Uncertain significance ★ same condition
NLRP3 p.Met1Val Uncertain significance ★ same residue
AVP p.Ala19Thr Pathogenic ★★ ⚠ same condition
AVP p.Cys92Tyr Likely pathogenic ★★ same condition
AVP p.Gly54Arg Pathogenic ★★ same condition
AVP p.Gly96Asp Pathogenic/Likely pathogenic ★★ same condition
AVP p.Ser87Phe Pathogenic/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/avp-p-met1fs (accessed [today's date]).

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