Is AVP p.Ser87Phe (c.260C>T) pathogenic?

AVP p.Ser87Phe (c.260C>T) is classified Pathogenic/Likely pathogenic in AVP (ClinVar, Multiple submitters, 3 submitters; last evaluated 2022-03-27). AlphaMissense: likely pathogenic (0.6038); Absent from gnomAD v4.1; Associated with AVP-related disorder.

What condition is associated with AVP p.Ser87Phe (c.260C>T)?

AVP p.Ser87Phe (c.260C>T) is associated with AVP-related disorder, neurohypophyseal diabetes insipidus (ClinVar).

How common is AVP p.Ser87Phe (c.260C>T) in the general population?

AVP p.Ser87Phe (c.260C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AVP p.Ser87Phe (c.260C>T)?

AlphaMissense predicts likely pathogenic (score 0.6038) — an in-silico prediction, not a clinical call.

AVP p.Ser87Phe

c.260C>T · rs121964890 · VCV12216

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.6038 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,560,010)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

AVP-related disorder

Computational evidence

Protein change
AlphaMissense	0.6038	likely pathogenic ✓ concordant with ClinVar
REVEL	0.732	pathogenic-leaning
SaProt	LLR -8.37	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7	GERP 0.65, phastCons 1
Overall
CADD	25.7	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

No allele count reported in gnomAD v4.1 (AN 1,560,010). 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.Ser87Phe
Coding: c.260C>T
MANE Select: NM_001243133 · reported on NM_000490
dbSNP: rs121964890
Type: single nucleotide variant
Location: chr20:3083039 (GRCh38)
Structure: AlphaFold pLDDT 81.16 · 27 PDB
Residue 87: the pyrin domain; an α-helix; a disulfide bond

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

Disease context

AVP-related disorder

Also linked: neurohypophyseal diabetes insipidus

Similar variants

AVP p.Ser87_Gln89del Uncertain significance ★ same residue
NLRP3 p.Arg87Lys Uncertain significance ★ ⚠ same residue
AVP p.Ser87Tyr Pathogenic/Likely pathogenic ⚠ same residue
AVP p.Ala19Thr Pathogenic ★★ ⚠ same condition
AVP p.Cys92Tyr Likely pathogenic ★★ same condition
AVP p.Glu108Ter Pathogenic ★★ same condition
AVP p.Gly54Arg Pathogenic ★★ same condition
AVP p.Gly96Asp 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-ser87phe (accessed [today's date]).

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