Is PRPS1 p.Pro276Ala (c.826C>G) pathogenic?

PRPS1 p.Pro276Ala (c.826C>G) is classified Likely pathogenic in PRPS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-09). AlphaMissense: likely pathogenic (0.6366); Absent from gnomAD v4.1; Associated with hearing loss, X-linked 1.

What condition is associated with PRPS1 p.Pro276Ala (c.826C>G)?

PRPS1 p.Pro276Ala (c.826C>G) is associated with hearing loss, X-linked 1 (ClinVar).

How common is PRPS1 p.Pro276Ala (c.826C>G) in the general population?

PRPS1 p.Pro276Ala (c.826C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PRPS1 p.Pro276Ala (c.826C>G)?

AlphaMissense predicts likely pathogenic (score 0.6366) — an in-silico prediction, not a clinical call.

PRPS1 p.Pro276Ala

c.826C>G · VCV3601703

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6366 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hearing loss, X-linked 1

Computational evidence

Protein change
AlphaMissense	0.6366	likely pathogenic ✓ concordant with ClinVar
REVEL	0.696	pathogenic-leaning
SaProt	LLR -13.09	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, phastCons 1
Regional constraint	o/e 0.37	unconstrained · MANE · 2,497 bp · p 1.3e-07 · regional, not allelic
Overall
CADD	26.1	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: PRPS1
Protein: p.Pro276Ala
Coding: c.826C>G
MANE Select: NM_002764
Type: single nucleotide variant
Location: chrX:107647727 (GRCh38)
Structure: AlphaFold pLDDT 94.77 · 27 PDB

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

Disease context

hearing loss, X-linked 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRPS1 p.Pro276Leu Likely pathogenic ★ same residue
PRPS1 p.Pro276His Uncertain significance ★ ⚠ same residue
PRPS1 p.Pro276Ser Likely pathogenic same residue
PRPS1 p.Met115Val Pathogenic/Likely pathogenic ★★ same condition
PRPS1 c.306+5G>T Uncertain significance ★★ same condition
PRPS1 c.*389G>A Uncertain significance ★★ same condition
PRPS1 p.Arg204His Uncertain significance ★★ same condition
PRPS1 p.Arg214Gln 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-pro276ala (accessed [today's date]).

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