UAP1L1

UDP-N-acetylglucosamine pyrophosphorylase 1 like 1

Basic information

Region (hg38): 9:137077517-137084539

Links

ENSG00000197355 ∙ NCBI:91373 ∙ ∙ HGNC:28082 ∙ Uniprot:Q3KQV9 ∙ 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 UAP1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UAP1L1 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			46	1		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	46	1	0

Variants in UAP1L1

This is a list of pathogenic ClinVar variants found in the UAP1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137077555-G-A		not specified	Uncertain significance (Dec 02, 2022)
9-137077561-G-A		not specified	Uncertain significance (Jan 03, 2024)
9-137077599-T-G		not specified	Uncertain significance (Aug 18, 2021)
9-137077623-C-G		not specified	Uncertain significance (Nov 13, 2023)
9-137077657-A-G		not specified	Uncertain significance (Oct 19, 2024)
9-137077677-C-T		not specified	Uncertain significance (Feb 22, 2023)
9-137077684-G-A		not specified	Uncertain significance (Dec 26, 2023)
9-137077690-C-G		not specified	Uncertain significance (Nov 15, 2021)
9-137077696-A-C		not specified	Likely benign (Oct 06, 2021)
9-137077715-C-A		not specified	Uncertain significance (Dec 19, 2022)
9-137077755-C-G		not specified	Uncertain significance (Jan 16, 2024)
9-137077759-C-G		not specified	Uncertain significance (Jun 29, 2022)
9-137077761-G-A		not specified	Uncertain significance (Feb 06, 2023)
9-137078055-C-T		not specified	Uncertain significance (Dec 20, 2023)
9-137078083-T-C		not specified	Uncertain significance (Sep 03, 2024)
9-137078092-T-G		not specified	Uncertain significance (Aug 20, 2024)
9-137078116-T-A		not specified	Uncertain significance (Jan 31, 2022)
9-137078135-G-C		not specified	Uncertain significance (Oct 11, 2024)
9-137078199-C-T		not specified	Uncertain significance (May 01, 2022)
9-137078214-C-G		not specified	Uncertain significance (Jan 30, 2024)
9-137078220-G-A		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
9-137078533-C-G		not specified	Uncertain significance (Dec 19, 2022)
9-137078565-C-A		not specified	Uncertain significance (Mar 25, 2022)
9-137078632-G-A		not specified	Uncertain significance (Jun 22, 2023)
9-137078982-A-G		not specified	Uncertain significance (Apr 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UAP1L1	protein_coding	protein_coding	ENST00000409858	9	7039

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000341	0.811	125658	0	55	125713	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.262	260	272	0.955	0.0000166	3224
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000583	0.000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000553	0.0000544
Finnish	0.0000937	0.0000924
European (Non-Finnish)	0.000264	0.000255
Middle Eastern	0.0000553	0.0000544
South Asian	0.000297	0.000294
Other	0.000332	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.784
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.251
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.240

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uap1l1

Gene ontology

• Biological process: UDP-N-acetylglucosamine biosynthetic process
• Molecular function: UDP-N-acetylglucosamine diphosphorylase activity