Is PRPS1 p.Val112= (c.336T>C) pathogenic?

PRPS1 p.Val112= (c.336T>C) is classified Likely benign in PRPS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-11). Absent from gnomAD v4.1; Associated with Nephrolithiasis/nephrocalcinosis.

What condition is associated with PRPS1 p.Val112= (c.336T>C)?

PRPS1 p.Val112= (c.336T>C) is associated with Nephrolithiasis/nephrocalcinosis (ClinVar).

How common is PRPS1 p.Val112= (c.336T>C) in the general population?

PRPS1 p.Val112= (c.336T>C) is absent from gnomAD v4.1 (gnomAD).

PRPS1 p.Val112=

c.336T>C · rs80338674 · VCV1730725

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Nephrolithiasis/nephrocalcinosis

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 -0.65	GERP -2.9, phastCons 0.038
Overall
CADD	6.265	PHRED · no single calibrated threshold — expert panels disagree

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.Val112=
Coding: c.336T>C
MANE Select: NM_002764
dbSNP: rs80338674
Type: single nucleotide variant
Location: chrX:107640931 (GRCh38)
Structure: AlphaFold pLDDT 94.77 · 27 PDB
Residue 112: an α-helix

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

Disease context

Nephrolithiasis/nephrocalcinosis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRPS1 p.Val112Ile Uncertain significance ★★ ⚠ same residue
PRPS1 p.Val112Leu Uncertain significance ⚠ same residue
PRPS1 p.Ala241Thr Uncertain significance ★★ ⚠ same condition
PRPS1 p.Val309Ile Uncertain significance ★★ ⚠ same condition
PRPS1 c.705-6C>T Benign/Likely benign ★★ same condition
PRPS1 p.Ala20= Likely benign ★★ same condition
PRPS1 p.Leu191= Benign/Likely benign ★★ same condition
PRPS1 p.Ser314= Benign/Likely benign ★★ 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-val112 (accessed [today's date]).

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