Is AZIN2 p.Ser31Pro (c.91T>C) pathogenic?

AZIN2 p.Ser31Pro (c.91T>C) is classified Uncertain significance in AZIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-02). AlphaMissense: likely benign (0.0864); Absent from gnomAD v4.1.

How common is AZIN2 p.Ser31Pro (c.91T>C) in the general population?

AZIN2 p.Ser31Pro (c.91T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AZIN2 p.Ser31Pro (c.91T>C)?

AlphaMissense predicts likely benign (score 0.0864) — an in-silico prediction, not a clinical call.

AZIN2 p.Ser31Pro

c.91T>C · rs1464843910 · VCV2207239

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0864 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0864	likely benign
REVEL	0.034	moderately benign-leaning
SaProt	LLR -13.00	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 1.5, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 36 kb · p 0.33 · regional, not allelic
Overall
CADD	21.4	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: AZIN2
Protein: p.Ser31Pro
Coding: c.91T>C
MANE Select: NM_052998
dbSNP: rs1464843910
Type: single nucleotide variant
Location: chr1:33082340 (GRCh38)
Gene constraint: LOEUF 0.797 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.94

Full AZIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AZIN2 p.His188Asn Benign ★★ same type
TRIM62 p.Glu234= Benign ★★ same type
TRIM62 p.Val473Ile Benign ★★ same type
AZIN2 p.Ala112Thr Uncertain significance ★ ⚠ same type
AZIN2 p.Arg217Gln Uncertain significance ★ ⚠ same type
AZIN2 p.Arg217Trp Uncertain significance ★ ⚠ same type
AZIN2 p.Arg412Trp Uncertain significance ★ ⚠ same type
AZIN2 p.Arg419Leu Uncertain significance ★ ⚠ 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/azin2-p-ser31pro (accessed [today's date]).

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