Is PRX p.Pro609Ser (c.1825C>T) pathogenic?

PRX p.Pro609Ser (c.1825C>T) is classified Uncertain significance in PRX (ClinVar, Single submitter, 1 submitter; last evaluated 2016-01-05). AlphaMissense: likely benign (0.1259); Absent from gnomAD v4.1.

How common is PRX p.Pro609Ser (c.1825C>T) in the general population?

PRX p.Pro609Ser (c.1825C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRX p.Pro609Ser (c.1825C>T)?

AlphaMissense predicts likely benign (score 0.1259) — an in-silico prediction, not a clinical call.

PRX p.Pro609Ser

c.1825C>T · rs759927281 · VCV234731

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1259 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1259	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -9.58	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 3.9	GERP -0.82, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 2,740 bp · p 0.15 · regional, not allelic
Overall
CADD	20.8	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: PRX
Protein: p.Pro609Ser
Coding: c.1825C>T
MANE Select: NM_181882
dbSNP: rs759927281
Type: single nucleotide variant
Location: chr19:40396527 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 35.74 · 1 PDB
Residue 609: 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

Similar variants

PRX p.Pro609= Likely benign ★★ same residue
PRX c.184+2T>C Likely pathogenic ★★ same type
PRX p.Arg1070Ter Pathogenic/Likely pathogenic ★★ same type
PRX p.Arg196Ter Pathogenic/Likely pathogenic ★★ same type
PRX p.Arg364Ter Pathogenic ★★ same type
PRX p.Arg368Ter Pathogenic/Likely pathogenic ★★ same type
PRX p.Arg392Ter Pathogenic/Likely pathogenic ★★ same type
PRX p.Arg464Ter Pathogenic/Likely pathogenic ★★ 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/prx-p-pro609ser (accessed [today's date]).

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