Is PRPS1 p.Phe253del (c.755TCT[1]) pathogenic?

PRPS1 p.Phe253del (c.755TCT[1]) is classified Uncertain significance in PRPS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-14). Absent from gnomAD; Associated with Charcot-Marie-Tooth Neuropathy X.

What condition is associated with PRPS1 p.Phe253del (c.755TCT[1])?

PRPS1 p.Phe253del (c.755TCT[1]) is associated with Charcot-Marie-Tooth Neuropathy X (ClinVar).

How common is PRPS1 p.Phe253del (c.755TCT[1]) in the general population?

PRPS1 p.Phe253del (c.755TCT[1]) is absent from gnomAD (gnomAD).

PRPS1 p.Phe253del

c.755TCT[1] · rs2521349580 · VCV2006649

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Charcot-Marie-Tooth Neuropathy X

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.2, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PRPS1
Protein: p.Phe253del
Coding: c.755TCT[1]
MANE Select: NM_002764
dbSNP: rs2521349580
Type: Microsatellite
Location: chrX:107647656 (GRCh38)
Structure: AlphaFold pLDDT 94.77 · 27 PDB

Full PRPS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

PRPS1 p.Phe253Tyr Uncertain significance ★ ⚠ same residue
PRPS1 p.Phe253= Likely benign ★ same residue
PRPS1 c.531-11_531-10del Likely benign ★ same condition
PRPS1 p.Ile107Val Likely pathogenic ★★ same condition
PRPS1 p.Met115Thr Pathogenic/Likely pathogenic ★★ same condition
PRPS1 p.Ser169Leu Pathogenic ★★ same condition
PRPS1 p.Ala216Thr Uncertain significance ★★ ⚠ same condition
PRPS1 p.Arg204Cys 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/prps1-p-phe253del (accessed [today's date]).

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