Pentosuria

Summary

Pentosuria (MONDO:0009846) is a disease with 1 cohort gene.

At a glance

• Prevalence: Unknown (Worldwide) [Orphanet-validated]
• Cohort genes: 1
• ClinVar variants: 2
• Phenotypes (HPO): 3

Clinical features

Signs & symptoms

Clinical features (HPO)

3 HPO clinical features (Orphanet curated; top 3 by frequency):

HPO ID	Term	Frequency
HP:0011021	Abnormality of circulating enzyme level	Very frequent (80-99%)
HP:0031979	Abnormal urine carbohydrate level	Very frequent (80-99%)
HP:0011013	Abnormal circulating carbohydrate concentration	Frequent (30-79%)

Identifiers

Disease identifiers

Field	Value
Canonical name	pentosuria
Mondo ID	MONDO:0009846
MeSH	C536652
OMIM	260800
Orphanet	2843
DOID	DOID:0111258
SNOMED CT	190764000
UMLS	C0268162
MedGen	78646
GARD	0000418
MedDRA	10064170
Is cancer (heuristic)	no

Also known as: essential pentosuria · pentosuria · PNTSU · xylitol dehydrogenase deficiency

Data availability: 2 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › inborn errors of metabolism › inborn carbohydrate metabolic disorder › disorders of pentose/polyol metabolism › inborn disorder of pentose phosphate metabolism › pentosuria

Related subtypes (5): anemia, nonspherocytic hemolytic, due to G6PD deficiency, transaldolase deficiency, ribose-5-P isomerase deficiency, transketolase deficiency, isolated sedoheptulokinase deficiency

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

2 retrieved; paginated sample, class counts are floors:

1 pathogenic; affects, 1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
101054	NM_016286.4(DCXR):c.583del (p.His195fs)	DCXR	Pathogenic; Affects	no assertion criteria provided
101055	NM_016286.4(DCXR):c.52+1G>A	DCXR	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 2 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
DCXR	Moderate	Autosomal recessive	pentosuria	2

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
DCXR	Orphanet:2843	Pentosuria

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
DCXR	HGNC:18985	ENSG00000169738	Q7Z4W1	L-xylulose reductase	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
DCXR	L-xylulose reductase	Catalyzes the NADPH-dependent reduction of several pentoses, tetroses, trioses, alpha-dicarbonyl compounds and L-xylulose.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Enzyme (other)	1	12.0×	0.083

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
DCXR	Enzyme (other)	yes	1.1.1.10	SDR_fam, Sc_DH/Rdtase_CS, NAD(P)-bd_dom_sf

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
corpus epididymis	1
liver	1
right lobe of liver	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
DCXR	279	ubiquitous	marker	right lobe of liver, liver, corpus epididymis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
DCXR	916

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
DCXR	Q7Z4W1	3

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 2. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Essential pentosuria	1	11420.0×	2e-04	DCXR
Formation of xylulose-5-phosphate	1	1903.3×	5e-04	DCXR

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
xylulose metabolic process	1	8426.0×	5e-04	DCXR
D-xylose metabolic process	1	5617.3×	5e-04	DCXR
obsolete D-glucuronate catabolic process to D-xylulose 5-phosphate	1	2808.7×	7e-04	DCXR
NADP+ metabolic process	1	1532.0×	1e-03	DCXR
positive regulation of reactive oxygen species metabolic process	1	510.7×	0.002	DCXR
glucose metabolic process	1	255.3×	0.004	DCXR

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
DCXR	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
DCXR	3	Binding:3

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
DCXR	1.1.1.10	L-xylulose reductase

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	1	DCXR
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
DCXR	3	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.