Is RTN2 p.Ala522Ser (c.1564G>T) pathogenic?

RTN2 p.Ala522Ser (c.1564G>T) is classified Uncertain significance in RTN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-20). AlphaMissense: likely benign (0.0995); Absent from gnomAD v4.1; Associated with RTN2-related disorder.

What condition is associated with RTN2 p.Ala522Ser (c.1564G>T)?

RTN2 p.Ala522Ser (c.1564G>T) is associated with RTN2-related disorder (ClinVar).

How common is RTN2 p.Ala522Ser (c.1564G>T) in the general population?

RTN2 p.Ala522Ser (c.1564G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about RTN2 p.Ala522Ser (c.1564G>T)?

AlphaMissense predicts likely benign (score 0.0995) — an in-silico prediction, not a clinical call.

RTN2 p.Ala522Ser

c.1564G>T · rs2513726432 · VCV2628393

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0995 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

RTN2-related disorder

Computational evidence

Protein change
AlphaMissense	0.0995	likely benign
REVEL	0.024	moderately benign-leaning
SaProt	LLR -6.34	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 0.85, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 11 kb · p 0.23 · regional, not allelic
Overall
CADD	22.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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: RTN2
Protein: p.Ala522Ser
Coding: c.1564G>T
MANE Select: NM_005619
dbSNP: rs2513726432
Type: single nucleotide variant
Location: chr19:45485782 (GRCh38)
Gene constraint: LOEUF 0.748 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.99
Residue 522: a UniProt-annotated variant site (in hmnr11; likely pathogenic); a UniProt-annotated variant site (in spg12; likely pathogenic); the reticulon domain

Full RTN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

RTN2-related disorder

Similar variants

RTN2 p.Gly148Val Uncertain significance ★ ⚠ same condition
RTN2 p.Glu50Ter Pathogenic/Likely pathogenic ★★ same type
RTN2 c.1497+3G>A Uncertain significance ★★ same type
RTN2 p.Ala529Thr Uncertain significance ★★ ⚠ same type
RTN2 p.Arg152Pro Uncertain significance ★★ ⚠ same type
RTN2 p.Arg252Trp Uncertain significance ★★ ⚠ same type
RTN2 p.Arg398Cys Uncertain significance ★★ ⚠ same type
RTN2 p.Arg406Trp 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/rtn2-p-ala522ser (accessed [today's date]).

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