Is PRX p.Val925= (c.2775C>T) pathogenic?

PRX p.Val925= (c.2775C>T) is classified Benign/Likely benign in PRX (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-11-21). Rare (popmax 0.844%, sas); Associated with Inborn genetic diseases.

What condition is associated with PRX p.Val925= (c.2775C>T)?

PRX p.Val925= (c.2775C>T) is associated with Inborn genetic diseases, Charcot-Marie-Tooth disease type 4F, Charcot-Marie-Tooth disease (ClinVar).

How common is PRX p.Val925= (c.2775C>T) in the general population?

PRX p.Val925= (c.2775C>T) is rare (popmax 0.844%, sas) (gnomAD).

PRX p.Val925=

c.2775C>T · rs201792838 · VCV329262

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

rare (popmax 0.844%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -2.6, phastCons 0.98
Overall
CADD	4.167	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.844% South Asian · 769/91,086 alleles

Filtering AF 0.795% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.775%

Overall 0.0514% 829/1,614,182 alleles · rare exomes 771/1,461,882 · genomes 58/152,300 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.844%	118
Remaining individualsnot grpmax-eligible	0.08%	1,250
African / African-American	0.00533%	18,760
East Asian	0.00446%	22,439
European (non-Finnish)	0.000339%	295,006

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PRX
Protein: p.Val925=
Coding: c.2775C>T
MANE Select: NM_181882
dbSNP: rs201792838
Type: single nucleotide variant
Location: chr19:40395577 (GRCh38)
Gene constraint: LOEUF 1.321 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 35.74 · 1 PDB

Full PRX 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

Also linked: Charcot-Marie-Tooth disease type 4F Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease type 4

Similar variants

PRX c.184+2T>C Likely pathogenic ★★ same condition
PRX p.Arg1070Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Arg196Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Arg364Ter Pathogenic ★★ same condition
PRX p.Arg368Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Arg392Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Arg464Ter Pathogenic/Likely pathogenic ★★ same condition
PRX p.Arg897Ter Pathogenic/Likely pathogenic ★★ 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-val925 (accessed [today's date]).

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