XYLB

protein-coding

xylulokinase

Gene summary

The protein encoded by this gene shares 22% sequence identity with Hemophilus influenzae xylulokinase, and even higher identity to other gene products in C.elegans (45%) and yeast (31-35%), which are thought to belong to a family of enzymes that include fucokinase, gluconokinase, glycerokinase and xylulokinase. These proteins play important roles in energy metabolism. [provided by RefSeq, Aug 2009]

MANE transcript

NM_005108.4

Inheritance

—

ClinVar variants

U:80B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr3:38,346,760-38,421,348

External References & Databases

Ensembl (ENSG00000093217)

Transcript & Mutation Effects

hg38 • Region Span ~74.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to XYLB variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005108.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			73 clinvar	5 clinvar	2 clinvar	80
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	80	6	2	88

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005108.4	RefSeq	NP_005099.2	19	MANE Select
ENST00000207870.8	Ensembl	ENSP00000207870.3	19	MANE Select
NM_001349178.2	RefSeq	NP_001336107.1	20	Standard
NM_001349179.2	RefSeq	NP_001336108.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pentose and glucuronate interconversions - Homo sapiens (human)
Metabolism of carbohydrates
Metabolism
Catabolism of glucuronate to xylulose-5-phosphate

Biological Process

carbohydrate metabolic process
xylulose metabolic process
xylulose catabolic process
generation of precursor metabolites and energy
phosphorylation

Molecular Function

xylulokinase activity
ATP binding

Cellular Component

cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000207870
Coding exons: 19
Length: 74589
Individuals with no LoFs: 125593
Homozygous LoFs: 0
Heterozygous LoFs: 155
Defined: 125748
p: 0.000616

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.210	299	309	0.966	0.0000170	3473
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0012	0.0012	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00055	0.00055	rare
South Asian	0.00054	0.00052	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.605
RVIS EVS: 0.67
RVIS percentile EVS: 84.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.939

Gene Damage Prediction

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