DCXR

dicarbonyl and L-xylulose reductase, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 17:82035136-82037709

Links

ENSG00000169738 ∙ NCBI:51181 ∙ OMIM:608347 ∙ HGNC:18985 ∙ Uniprot:Q7Z4W1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• pentosuria (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pentosuria	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical	22042873

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DCXR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCXR gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	18	2	2

Variants in DCXR

This is a list of pathogenic ClinVar variants found in the DCXR region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-82035971-A-C		not specified	Uncertain significance (Jan 26, 2022)
17-82035989-G-C		not specified	Uncertain significance (Oct 03, 2022)
17-82036007-T-A		not specified	Uncertain significance (Oct 05, 2023)
17-82036061-C-T		DCXR-related disorder	Likely benign (Apr 15, 2022)
17-82036235-T-G		not specified	Uncertain significance (May 12, 2024)
17-82036238-T-C		not specified	Uncertain significance (Dec 08, 2023)
17-82036238-TG-T		Essential pentosuria • DCXR-related disorder	Pathogenic; Affects (Mar 23, 2024)
17-82036419-T-C		not specified	Uncertain significance (Aug 30, 2021)
17-82036434-C-A		not specified	Uncertain significance (Dec 20, 2023)
17-82036632-C-G		not specified	Uncertain significance (Jun 29, 2023)
17-82036634-T-C		not specified	Uncertain significance (Aug 08, 2023)
17-82036724-C-T		DCXR-related disorder	Benign (Oct 28, 2019)
17-82036748-G-T		not specified	Uncertain significance (Aug 15, 2023)
17-82036754-C-G		not specified	Likely benign (Jul 07, 2022)
17-82036904-G-A		not specified	Uncertain significance (Mar 01, 2024)
17-82036950-C-T		not specified	Likely benign (Nov 29, 2024)
17-82037444-A-G		DCXR-related disorder	Benign (Oct 28, 2019)
17-82037455-G-A		not specified	Uncertain significance (Jun 02, 2023)
17-82037458-C-G		not specified	Uncertain significance (Aug 19, 2024)
17-82037473-C-A		not specified	Uncertain significance (Sep 26, 2024)
17-82037482-T-C		not specified	Uncertain significance (Nov 10, 2022)
17-82037482-T-G		not specified	Uncertain significance (May 11, 2022)
17-82037486-G-C		not specified	Uncertain significance (May 11, 2022)
17-82037511-G-A		not specified	Uncertain significance (Dec 13, 2023)
17-82037555-G-A			Benign (Jun 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCXR	protein_coding	protein_coding	ENST00000306869	8	2597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.35e-7	0.312	125549	0	76	125625	0.000303

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.121	140	144	0.972	0.00000863	1540
Missense in Polyphen		35	49.482	0.70732		536
Synonymous	0.0702	63	63.7	0.989	0.00000414	535
Loss of Function	0.367	10	11.3	0.882	5.83e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000559	0.000532
Ashkenazi Jewish	0.00	0.00
East Asian	0.000928	0.000925
Finnish	0.000519	0.000508
European (Non-Finnish)	0.000258	0.000255
Middle Eastern	0.000928	0.000925
South Asian	0.0000665	0.0000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the NADPH-dependent reduction of several pentoses, tetroses, trioses, alpha-dicarbonyl compounds and L- xylulose. Participates in the uronate cycle of glucose metabolism. May play a role in the water absorption and cellular osmoregulation in the proximal renal tubules by producing xylitol, an osmolyte, thereby preventing osmolytic stress from occurring in the renal tubules.
• Pathway: Pentose and glucuronate interconversions - Homo sapiens (human);Metabolism of carbohydrates;Metabolism;D-glucuronate degradation;Catabolism of glucuronate to xylulose-5-phosphate (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.783
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.0752
• hipred: N
• hipred_score: 0.349
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dcxr

Gene ontology

• Biological process: xylulose metabolic process;glucose metabolic process;NADP metabolic process;glucuronate catabolic process to xylulose 5-phosphate;D-xylose metabolic process;protein homotetramerization;oxidation-reduction process
• Cellular component: nucleus;cytoplasmic microtubule;plasma membrane;microvillus;brush border;extracellular exosome
• Molecular function: carbonyl reductase (NADPH) activity;oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor;identical protein binding;L-xylulose reductase (NAD+) activity;L-xylulose reductase (NADP+) activity