Is ANO3 p.Pro515Ala (c.1543C>G) pathogenic?

ANO3 p.Pro515Ala (c.1543C>G) is classified Uncertain significance in ANO3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-01). AlphaMissense: likely pathogenic (0.6322); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with ANO3 p.Pro515Ala (c.1543C>G)?

ANO3 p.Pro515Ala (c.1543C>G) is associated with Inborn genetic diseases (ClinVar).

How common is ANO3 p.Pro515Ala (c.1543C>G) in the general population?

ANO3 p.Pro515Ala (c.1543C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ANO3 p.Pro515Ala (c.1543C>G)?

AlphaMissense predicts likely pathogenic (score 0.6322) — an in-silico prediction, not a clinical call.

ANO3 p.Pro515Ala

c.1543C>G · VCV4110973

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6322 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.6322	likely pathogenic
REVEL	0.504	indeterminate
SaProt	LLR -11.27	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.8, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 129 kb · p 7.8e-20 · regional, not allelic
Overall
CADD	26.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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: ANO3
Protein: p.Pro515Ala
Coding: c.1543C>G
MANE Select: NM_031418
Type: single nucleotide variant
Location: chr11:26598870 (GRCh38)
Gene constraint: LOEUF 0.911 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.30

Full ANO3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ANO3 p.Ile607Phe Pathogenic/Likely pathogenic ★★ same condition
ANO3 p.Ala41Ser Uncertain significance ★★ ⚠ same condition
ANO3 p.Ala41Thr Uncertain significance ★★ ⚠ same condition
ANO3 p.Arg125His Uncertain significance ★★ ⚠ same condition
ANO3 p.Arg305Gln Uncertain significance ★★ ⚠ same condition
ANO3 p.Arg34Gln Uncertain significance ★★ ⚠ same condition
ANO3 p.Arg368Cys Uncertain significance ★★ ⚠ same condition
ANO3 p.Arg969Trp Uncertain significance ★★ 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/ano3-p-pro515ala (accessed [today's date]).

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