IMPDH2

inosine monophosphate dehydrogenase 2

Basic information

Region (hg38): 3:49024325-49029447

Links

ENSG00000178035

∙ NCBI:3615 ∙ OMIM:146691 ∙ HGNC:6053 ∙ Uniprot:P12268 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
IMPDH2 enzyme activity, variation in	AD	Pharmacogenomic	Variants may be involved in response to treatment with medications such as mycophenolate mofetil in individuals who have undergone transplants	Biochemical	17496727

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IMPDH2 gene.

not_provided (35 variants)
not_specified (29 variants)
IMPDH2-related_disorder (3 variants)
Dystonic_disorder (2 variants)
IMPDH2-associated_neurodevelopmental_disorder (1 variants)
IMPDH2-related_neurodevelopmental_condition (1 variants)
IMPDH2_enzyme_activity,_variation_in (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IMPDH2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000884.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense		4 clinvar	54 clinvar			58
nonsense			1 clinvar			1
start loss						0
frameshift		1 clinvar	3 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	0	5	58	0	0

Highest pathogenic variant AF is 0.0000056257595

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IMPDH2	protein_coding	protein_coding	ENST00000326739	14	5084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000436	0.991	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	176	297	0.592	0.0000173	3367
Missense in Polyphen		46	114.97	0.40011		1301
Synonymous	-0.931	123	111	1.11	0.00000597	1021
Loss of Function	2.35	13	25.9	0.502	0.00000129	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000517	0.000454
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000549	0.000544
Finnish	0.000198	0.000185
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000549	0.000544
South Asian	0.000392	0.000392
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the conversion of inosine 5'-phosphate (IMP) to xanthosine 5'-phosphate (XMP), the first committed and rate- limiting step in the de novo synthesis of guanine nucleotides, and therefore plays an important role in the regulation of cell growth. Could also have a single-stranded nucleic acid-binding activity and could play a role in RNA and/or DNA metabolism. It may also have a role in the development of malignancy and the growth progression of some tumors.;
Pathway: Drug metabolism - other enzymes - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Mycophenolic acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics/Pharmacodynamics;Mycophenolic Acid Metabolism Pathway;Neutrophil degranulation;Metabolism of nucleotides;urate biosynthesis/inosine 5,-phosphate degradation;purine nucleotides degradation;Innate Immune System;Immune System;Metabolism;Nucleobase biosynthesis;Purine nucleotides nucleosides metabolism;superpathway of purine nucleotide salvage;Purine ribonucleoside monophosphate biosynthesis;guanosine nucleotides de novo biosynthesis;guanosine ribonucleotides de novo biosynthesis;purine nucleotides de novo biosynthesis (Consensus)

Recessive Scores

pRec: 0.394

Intolerance Scores

loftool: 0.581
rvis_EVS: -0.65
rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

pHI: 0.965
hipred: Y
hipred_score: 0.701
ghis: 0.610

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Impdh2
Phenotype: immune system phenotype; cellular phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name: impdh2
Affected structure: whole organism
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

Biological process: GMP biosynthetic process;GTP biosynthetic process;circadian rhythm;purine ribonucleoside monophosphate biosynthetic process;neutrophil degranulation;lymphocyte proliferation;protein homotetramerization;oxidation-reduction process;retina development in camera-type eye;cellular response to interleukin-4
Cellular component: extracellular region;nucleus;cytoplasm;peroxisomal membrane;cytosol;membrane;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
Molecular function: nucleotide binding;DNA binding;RNA binding;IMP dehydrogenase activity;protein binding;metal ion binding