UAP1L1

protein-coding

UDP-N-acetylglucosamine pyrophosphorylase 1 like 1

Gene summary

Predicted to enable UDP-N-acetylglucosamine diphosphorylase activity. Predicted to be involved in UDP-N-acetylglucosamine biosynthetic process. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_207309.3

Inheritance

—

ClinVar variants

U:88B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr9:137,077,517-137,084,539

External References & Databases

Ensembl (ENSG00000197355)

Transcript & Mutation Effects

hg38 • Region Span ~7.0 kb

Loading mutation effect viewer...

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 UAP1L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207309.3. 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			86 clinvar	4 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	88	5	0	93

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207309.3	RefSeq	NP_997192.2	9	MANE Select
ENST00000409858.8	Ensembl	ENSP00000386935.3	9	MANE Select
ENST00000360271.3	Ensembl	ENSP00000353409.3	7	Standard
ENST00000360271.4	Ensembl	ENSP00000353409.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Amino sugar and nucleotide sugar metabolism - Homo sapiens (human)

Biological Process

UDP-N-acetylglucosamine biosynthetic process

Molecular Function

UDP-N-acetylglucosamine diphosphorylase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409858
Coding exons: 9
Length: 7039
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 55
Defined: 125713
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.262	260	272	0.955	0.0000166	3224
Missense (PolyPhen)		120	138.48	0.86657		1458
Synonymous	0.611	113	122	0.929	0.00000791	1088
Loss of Function	1.34	11	17.0	0.649	8.02e-7	220

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00026	0.00026	rare
South Asian	0.00030	0.00029	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.784
RVIS EVS: -0.22
RVIS percentile EVS: 37.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.240

Gene Damage Prediction

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