GMPR

guanosine monophosphate reductase

Basic information

Region (hg38): 6:16238586-16295549

Links

ENSG00000137198 ∙ NCBI:2766 ∙ OMIM:139265 ∙ HGNC:4376 ∙ Uniprot:P36959 ∙ 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 GMPR gene.

• Inborn genetic diseases (14 variants)
• not provided (6 variants)
• GMP REDUCTASE POLYMORPHISM (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GMPR 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
missense			14		2	16
nonsense						0
start loss						0
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	5

Variants in GMPR

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

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

Position	Type	Phenotype	Significance	ClinVar
6-16238700-C-G		not specified	Uncertain significance (Aug 10, 2021)
6-16238729-C-A		not specified	Uncertain significance (May 01, 2022)
6-16238749-C-T		not specified	Uncertain significance (Apr 11, 2023)
6-16246950-G-A		not specified	Uncertain significance (Sep 01, 2021)
6-16250323-G-A		not specified	Uncertain significance (Dec 11, 2023)
6-16250348-A-C		not specified	Uncertain significance (Oct 05, 2023)
6-16254571-G-A		not specified	Uncertain significance (Aug 13, 2021)
6-16254601-G-A		not specified	Uncertain significance (Sep 25, 2023)
6-16254625-G-T		not specified	Uncertain significance (May 03, 2023)
6-16254707-G-A		not specified	Uncertain significance (Jul 13, 2021)
6-16254730-A-G		not specified	Uncertain significance (Oct 12, 2021)
6-16274423-C-T			Benign (Dec 14, 2017)
6-16274479-A-G		not specified	Uncertain significance (Jul 15, 2021)
6-16278873-A-G		not specified	Uncertain significance (Sep 28, 2021)
6-16278885-A-G		not specified	Uncertain significance (Mar 23, 2023)
6-16285833-T-G		not specified	Uncertain significance (Jun 08, 2022)
6-16290511-G-A			Benign (Dec 14, 2017)
6-16290530-T-A		GMP REDUCTASE POLYMORPHISM	Benign (Jul 13, 2018)
6-16290542-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-16290550-G-C		not specified	Uncertain significance (Aug 30, 2022)
6-16290617-T-TAC			Likely benign (Dec 31, 2019)
6-16295006-A-T		not specified	Uncertain significance (Aug 14, 2023)
6-16295016-G-C		not specified	Uncertain significance (Jul 12, 2023)
6-16295047-A-T			Benign (Dec 31, 2019)
6-16295116-A-AACTC			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GMPR	protein_coding	protein_coding	ENST00000259727	9	56970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000131	0.849	124906	7	835	125748	0.00335

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.124	198	203	0.976	0.0000118	2249
Missense in Polyphen		92	95.911	0.95922		1071
Synonymous	-0.575	89	82.4	1.08	0.00000552	688
Loss of Function	1.39	10	16.0	0.624	7.55e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000474	0.000474
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0249	0.0194
Finnish	0.00365	0.00366
European (Non-Finnish)	0.00309	0.00309
Middle Eastern	0.0249	0.0194
South Asian	0.000663	0.000588
Other	0.00439	0.00424

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. {ECO:0000255|HAMAP-Rule:MF_03195}.
• Pathway: Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;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;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Metabolism of nucleotides;Metabolism;Nucleotide salvage;Purine salvage;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.219

Intolerance Scores

• loftool: 0.480
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.565
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gmpr

Gene ontology

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