GMPS

guanine monophosphate synthase, the group of Glutamine amidotransferase class 1 domain containing

Basic information

Region (hg38): 3:155870649-155944020

Links

ENSG00000163655 ∙ NCBI:8833 ∙ OMIM:600358 ∙ HGNC:4378 ∙ Uniprot:P49915 ∙ 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 GMPS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMPS 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					3	3
missense			26		1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	26	0	5

Variants in GMPS

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

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

Position	Type	Phenotype	Significance	ClinVar
3-155870895-A-C		not specified	Uncertain significance (Nov 13, 2023)
3-155870906-G-T			Benign (Dec 31, 2019)
3-155893564-A-T		not specified	Uncertain significance (Sep 12, 2023)
3-155893698-C-T		not specified	Uncertain significance (Mar 11, 2022)
3-155893704-A-G			Benign (Dec 31, 2019)
3-155897934-A-G		not specified	Uncertain significance (Apr 28, 2022)
3-155903941-A-G		not specified	Uncertain significance (Jun 02, 2023)
3-155906242-C-T		not specified	Uncertain significance (Feb 17, 2024)
3-155906261-C-A		not specified	Uncertain significance (May 03, 2023)
3-155910748-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-155910818-C-T		not specified	Uncertain significance (Aug 02, 2023)
3-155910873-G-A			Benign (Dec 31, 2019)
3-155911256-A-G		not specified	Uncertain significance (Jul 12, 2022)
3-155911265-G-A		not specified	Uncertain significance (Apr 19, 2024)
3-155914509-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-155914549-C-T			Benign (Dec 31, 2019)
3-155914560-C-A		not specified	Uncertain significance (Oct 05, 2021)
3-155916180-G-T		not specified	Uncertain significance (Nov 17, 2022)
3-155922241-A-C		not specified	Uncertain significance (Feb 06, 2024)
3-155925257-A-G		not specified	Uncertain significance (Dec 07, 2023)
3-155925365-A-G		not specified	Uncertain significance (Jun 24, 2022)
3-155931774-C-T		not specified	Uncertain significance (Nov 13, 2023)
3-155931787-A-C			Benign (Jun 18, 2018)
3-155931790-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-155931859-G-A		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMPS	protein_coding	protein_coding	ENST00000496455	16	73491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00175	124642	0	9	124651	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.37	228	353	0.645	0.0000174	4522
Missense in Polyphen		66	145.51	0.45359		1834
Synonymous	1.12	101	116	0.868	0.00000553	1332
Loss of Function	4.73	3	31.7	0.0945	0.00000165	430

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000559	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000442
Middle Eastern	0.0000559	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the de novo synthesis of guanine nucleotides which are not only essential for DNA and RNA synthesis, but also provide GTP, which is involved in a number of cellular processes important for cell division.
• Disease: DISEASE: Note=A chromosomal aberration involving GMPS is found in acute myeloid leukemias. Translocation t(3,11)(q25,q23) with KMT2A/MLL1.
• Pathway: Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;2-Hydroxyglutric Aciduria (D And L Form);Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Homocarnosinosis;Hyperinsulinism-Hyperammonemia Syndrome;Succinic semialdehyde dehydrogenase deficiency;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Mercaptopurine Metabolism Pathway;4-Hydroxybutyric Aciduria/Succinic Semialdehyde Dehydrogenase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Glutamate Metabolism;Metabolism of nucleotides;Metabolism;Nucleobase biosynthesis;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;Purine ribonucleoside monophosphate biosynthesis;guanosine nucleotides <i>de novo</i> biosynthesis;guanosine ribonucleotides <i>de novo</i> biosynthesis;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.533

Intolerance Scores

• loftool: 0.252
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.831
• hipred: Y
• hipred_score: 0.853
• ghis: 0.659

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmps

Zebrafish Information Network

• Gene name: gmps
• Affected structure: iridophore
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: GMP biosynthetic process;glutamine metabolic process;purine nucleobase biosynthetic process;purine ribonucleoside monophosphate biosynthetic process
• Cellular component: cytosol
• Molecular function: GMP synthase activity;GMP synthase (glutamine-hydrolyzing) activity;ATP binding;pyrophosphatase activity