GMPR2

guanosine monophosphate reductase 2

Basic information

Region (hg38): 14:24232422-24239242

Links

ENSG00000100938 ∙ NCBI:51292 ∙ OMIM:610781 ∙ HGNC:4377 ∙ Uniprot:Q9P2T1 ∙ 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 GMPR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMPR2 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in GMPR2

This is a list of pathogenic ClinVar variants found in the GMPR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24233215-C-A		not specified	Uncertain significance (Sep 29, 2023)
14-24233522-C-T		not specified	Uncertain significance (Oct 21, 2021)
14-24233557-G-A		not specified	Uncertain significance (Jan 26, 2022)
14-24233594-G-T		not specified	Uncertain significance (Mar 06, 2023)
14-24235798-G-T		not specified	Uncertain significance (Jul 09, 2021)
14-24236040-A-G		not specified	Uncertain significance (Nov 19, 2022)
14-24236090-G-A		not specified	Uncertain significance (Aug 13, 2021)
14-24236102-A-G		not specified	Uncertain significance (Jun 17, 2024)
14-24236112-G-A		not specified	Uncertain significance (Aug 13, 2021)
14-24237260-C-T		not specified	Uncertain significance (Apr 28, 2022)
14-24238260-T-C		not specified	Uncertain significance (Dec 19, 2023)
14-24238268-G-C		not specified	Uncertain significance (May 17, 2023)
14-24238360-C-T			Uncertain significance (-)
14-24238396-C-T		not specified	Uncertain significance (Jun 18, 2021)
14-24238402-A-C		not specified	Uncertain significance (May 18, 2023)
14-24238600-G-A		not specified	Uncertain significance (Mar 19, 2024)
14-24238635-G-C		not specified	Uncertain significance (Apr 22, 2024)
14-24238704-A-G		not specified	Uncertain significance (Dec 21, 2023)
14-24238720-G-A		not specified	Uncertain significance (Jan 17, 2023)
14-24238735-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMPR2	protein_coding	protein_coding	ENST00000420554	9	6821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-8	0.321	124731	0	95	124826	0.000381

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.800	177	210	0.845	0.0000106	2399
Missense in Polyphen		65	78.441	0.82865		912
Synonymous	-0.261	78	75.1	1.04	0.00000383	726
Loss of Function	0.705	14	17.1	0.816	8.50e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000570	0.000570
Ashkenazi Jewish	0.00	0.00
East Asian	0.000389	0.000389
Finnish	0.00	0.00
European (Non-Finnish)	0.000583	0.000583
Middle Eastern	0.000389	0.000389
South Asian	0.0000981	0.0000980
Other	0.000495	0.000494

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the irreversible NADPH-dependent deamination of GMP to IMP. It functions in the conversion of nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and in maintaining the intracellular balance of A and G nucleotides (PubMed:12009299, PubMed:12669231, PubMed:16359702, PubMed:22037469). Plays a role in modulating cellular differentiation (PubMed:12669231). {ECO:0000255|HAMAP- Rule:MF_03195, ECO:0000269|PubMed:12009299, ECO:0000269|PubMed:12669231, ECO:0000269|PubMed:16359702, ECO:0000269|PubMed:22037469}.
• Pathway: Purine metabolism - Homo sapiens (human);Metabolism of nucleotides;Metabolism;Nucleotide salvage;Purine salvage;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.249

Intolerance Scores

• loftool: 0.454
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.0865
• hipred: Y
• hipred_score: 0.504
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmpr2

Gene ontology

• Biological process: purine nucleobase metabolic process;purine ribonucleotide interconversion;purine-containing compound salvage;GMP metabolic process;oxidation-reduction process
• Cellular component: cytosol;GMP reductase complex
• Molecular function: GMP reductase activity;metal ion binding