UAP1

UDP-N-acetylglucosamine pyrophosphorylase 1

Basic information

Region (hg38): 1:162561722-162601240

Previous symbols: [ "SPAG2" ]

Links

ENSG00000117143 ∙ NCBI:6675 ∙ OMIM:602862 ∙ HGNC:12457 ∙ Uniprot:Q16222 ∙ 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 UAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UAP1 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	4
missense			30		2	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	30	2	5

Variants in UAP1

This is a list of pathogenic ClinVar variants found in the UAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-162566083-C-A		not specified	Uncertain significance (Jan 31, 2023)
1-162566099-T-C		not specified	Uncertain significance (Dec 31, 2023)
1-162566247-C-T		not specified	Uncertain significance (Jul 06, 2024)
1-162566289-G-A		not specified	Uncertain significance (Sep 02, 2024)
1-162566289-G-T		not specified	Uncertain significance (Jun 21, 2023)
1-162566298-T-C		not specified	Uncertain significance (Apr 23, 2024)
1-162566315-G-A		not specified	Uncertain significance (Oct 09, 2024)
1-162566344-T-G		not specified	Uncertain significance (May 27, 2022)
1-162576779-C-T		not specified	Uncertain significance (Dec 13, 2023)
1-162576815-C-A		not specified	Uncertain significance (Oct 12, 2022)
1-162576865-G-A			Likely benign (Jun 01, 2022)
1-162576866-A-T		not specified	Uncertain significance (Dec 11, 2024)
1-162576896-A-C		not specified	Uncertain significance (Apr 13, 2022)
1-162576920-C-T		not specified	Uncertain significance (May 28, 2024)
1-162576990-C-T			Benign (Dec 31, 2019)
1-162579516-A-G		not specified	Uncertain significance (Aug 02, 2023)
1-162581388-A-G		not specified	Uncertain significance (Jan 29, 2025)
1-162581413-G-A		not specified	Uncertain significance (Apr 24, 2024)
1-162581442-G-T		not specified	Uncertain significance (Oct 20, 2024)
1-162587502-C-G		not specified	Uncertain significance (Jan 23, 2024)
1-162587514-G-A		not specified	Uncertain significance (Jun 23, 2023)
1-162587568-G-C		not specified	Uncertain significance (Jul 12, 2023)
1-162587615-G-A			Benign (Dec 31, 2019)
1-162587637-T-C		not specified	Uncertain significance (May 27, 2022)
1-162588697-T-G		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UAP1	protein_coding	protein_coding	ENST00000367926	9	38305

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0234	0.977	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	226	274	0.826	0.0000139	3354
Missense in Polyphen		71	110.09	0.64493		1359
Synonymous	-1.48	111	92.8	1.20	0.00000447	928
Loss of Function	3.37	8	26.8	0.298	0.00000167	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts UTP and GlcNAc-1-P into UDP-GlcNAc, and UTP and GalNAc-1-P into UDP-GalNAc. Isoform AGX1 has 2 to 3 times higher activity towards GalNAc-1-P, while isoform AGX2 has 8 times more activity towards GlcNAc-1-P.
• Pathway: UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II;Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;UDP-<i>N</i>-acetyl-D-glucosamine biosynthesis II;Synthesis of UDP-N-acetyl-glucosamine;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.528
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• pHI: 0.339
• hipred: Y
• hipred_score: 0.654
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.898

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uap1

Gene ontology

• Biological process: UDP-N-acetylglucosamine biosynthetic process
• Cellular component: nucleoplasm;cytosol;plasma membrane
• Molecular function: UDP-N-acetylglucosamine diphosphorylase activity;carbohydrate binding;identical protein binding