Is PRX p.Val766Ala (c.2297T>C) pathogenic?

PRX p.Val766Ala (c.2297T>C) is classified Uncertain significance in PRX (ClinVar, Single submitter, 1 submitter). AlphaMissense: likely benign (0.2813); Absent from gnomAD v4.1; Associated with Charcot-Marie-Tooth disease.

What condition is associated with PRX p.Val766Ala (c.2297T>C)?

PRX p.Val766Ala (c.2297T>C) is associated with Charcot-Marie-Tooth disease (ClinVar).

How common is PRX p.Val766Ala (c.2297T>C) in the general population?

PRX p.Val766Ala (c.2297T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRX p.Val766Ala (c.2297T>C)?

AlphaMissense predicts likely benign (score 0.2813) — an in-silico prediction, not a clinical call.

PRX p.Val766Ala

c.2297T>C · rs1599653064 · VCV917236

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2813 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Charcot-Marie-Tooth disease

Computational evidence

Protein change
AlphaMissense	0.2813	likely benign
REVEL	0.13	moderately benign-leaning
SaProt	LLR -10.20	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 11	GERP 2.1, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 2,740 bp · p 0.15 · regional, not allelic
Overall
CADD	23.4	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: PRX
Protein: p.Val766Ala
Coding: c.2297T>C
MANE Select: NM_181882
dbSNP: rs1599653064
Type: single nucleotide variant
Location: chr19:40396055 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 35.74 · 1 PDB
Residue 766: the '55 x 5 aa approximate tandem repeats of [lvmag]-[psreqc]-[edkl]-[livmap]-[aqkhrpe]; that may have a tripeptide spacer of [lv]-p-[ker]' region

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

Disease context

Charcot-Marie-Tooth disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRX p.Val766Met Uncertain significance ★★ ⚠ same residue
PRX p.Arg196Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Arg364Ter Pathogenic ★★ same condition
PRX p.Arg953Ter Pathogenic ★★ same condition
PRX p.Cys715Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Gln622Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Glu197Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Ala1000Val 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/prx-p-val766ala (accessed [today's date]).

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