XYLB

xylulokinase

Basic information

Region (hg38): 3:38346759-38421348

Links

ENSG00000093217 ∙ NCBI:9942 ∙ OMIM:604049 ∙ HGNC:12839 ∙ Uniprot:O75191 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (24 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XYLB 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						0
missense			20	4	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	4	2

Variants in XYLB

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

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

Position	Type	Phenotype	Significance	ClinVar
3-38346882-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-38348563-C-T		not specified	Uncertain significance (Sep 15, 2021)
3-38360349-G-A		not specified	Uncertain significance (Jul 06, 2021)
3-38362967-G-A		not specified	Uncertain significance (Dec 03, 2021)
3-38362979-G-A		not specified	Uncertain significance (Dec 16, 2023)
3-38363006-G-A		not specified	Uncertain significance (Feb 02, 2022)
3-38363009-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-38365209-G-A		not specified	Uncertain significance (Dec 16, 2022)
3-38365248-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-38365626-G-A			Benign (Apr 10, 2018)
3-38365627-A-G		not specified	Uncertain significance (Mar 16, 2022)
3-38365641-A-T		not specified	Uncertain significance (Oct 05, 2023)
3-38366846-G-C		not specified	Uncertain significance (Jan 04, 2022)
3-38368247-C-G		not specified	Uncertain significance (Dec 28, 2023)
3-38372677-T-C		not specified	Uncertain significance (Jun 13, 2023)
3-38372682-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-38374462-C-T		not specified	Uncertain significance (Dec 06, 2022)
3-38374465-C-T		not specified	Uncertain significance (Jan 17, 2024)
3-38375226-C-A		not specified	Uncertain significance (Sep 12, 2023)
3-38376154-A-G			Benign (Apr 10, 2018)
3-38376965-C-T		not specified	Uncertain significance (Sep 13, 2023)
3-38376978-C-T		not specified	Uncertain significance (Jun 13, 2023)
3-38379261-G-A		not specified	Likely benign (May 17, 2023)
3-38379262-G-A		not specified	Uncertain significance (Dec 05, 2022)
3-38397103-A-G		not specified	Uncertain significance (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XYLB	protein_coding	protein_coding	ENST00000207870	19	74589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-22	0.00123	125593	0	155	125748	0.000616

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.210	299	309	0.966	0.0000170	3473
Missense in Polyphen		84	83.117	1.0106		914
Synonymous	0.0972	116	117	0.989	0.00000704	1041
Loss of Function	0.118	34	34.8	0.978	0.00000170	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00150	0.00150
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00120	0.00120
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000546	0.000545
Middle Eastern	0.00120	0.00120
South Asian	0.000543	0.000523
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates D-xylulose to produce D-xylulose 5- phosphate, a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis. {ECO:0000269|PubMed:23179721}.
• Pathway: Pentose and glucuronate interconversions - Homo sapiens (human);Metabolism of carbohydrates;Metabolism;Catabolism of glucuronate to xylulose-5-phosphate (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.605
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.68

Haploinsufficiency Scores

• pHI: 0.360
• hipred: N
• hipred_score: 0.167
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.939

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xylb
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;xylulose metabolic process;xylulose catabolic process;generation of precursor metabolites and energy;phosphorylation;glucuronate catabolic process to xylulose 5-phosphate;D-xylose metabolic process;carbohydrate phosphorylation
• Cellular component: cytoplasm;cytosol
• Molecular function: xylulokinase activity;ATP binding