MPG

N-methylpurine DNA glycosylase, the group of DNA glycosylases

Basic information

Region (hg38): 16:77007-85851

Links

ENSG00000103152 ∙ NCBI:4350 ∙ OMIM:156565 ∙ HGNC:7211 ∙ Uniprot:P29372 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPG 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			40	1		41
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	2

Variants in MPG

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

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

Position	Type	Phenotype	Significance	ClinVar
16-79429-G-T		not specified	Uncertain significance (Nov 19, 2022)
16-79458-C-G		not specified	Uncertain significance (Mar 29, 2024)
16-79459-C-T		not specified	Likely benign (Feb 05, 2024)
16-79479-C-A		not specified	Uncertain significance (Aug 05, 2024)
16-79493-C-T			Benign (Aug 16, 2018)
16-79533-G-C		not specified	Uncertain significance (Feb 23, 2025)
16-79557-A-T		not specified	Uncertain significance (Sep 03, 2024)
16-79564-G-A		not specified	Uncertain significance (Sep 24, 2024)
16-79589-G-A			Benign (Aug 16, 2018)
16-79602-A-G		not specified	Uncertain significance (Jan 29, 2024)
16-79639-G-A		not specified	Uncertain significance (Apr 13, 2023)
16-79647-T-A		not specified	Uncertain significance (Dec 28, 2023)
16-79660-A-C		not specified	Uncertain significance (Dec 02, 2024)
16-79677-CT-C		MPG-related condition	Uncertain significance (Jun 21, 2023)
16-79687-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-83062-G-A		not specified	Uncertain significance (Jul 15, 2021)
16-83097-A-G		not specified	Uncertain significance (Mar 31, 2023)
16-83100-G-A		not specified	Uncertain significance (Aug 02, 2021)
16-83118-C-A		not specified	Uncertain significance (Jul 20, 2022)
16-83118-C-G		not specified	Uncertain significance (Dec 20, 2024)
16-83121-G-T		not specified	Uncertain significance (Mar 07, 2024)
16-83128-A-G		not specified	Uncertain significance (Feb 11, 2022)
16-83221-A-G		not specified	Uncertain significance (Dec 21, 2023)
16-83223-G-A		not specified	Uncertain significance (Aug 10, 2021)
16-83224-G-T		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPG	protein_coding	protein_coding	ENST00000219431	4	8847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-12	0.0171	125350	1	383	125734	0.00153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.489	220	201	1.10	0.0000137	1883
Missense in Polyphen		98	80.575	1.2163		732
Synonymous	-2.24	107	81.3	1.32	0.00000537	647
Loss of Function	-0.404	17	15.3	1.11	0.00000125	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00132	0.00131
Ashkenazi Jewish	0.00570	0.00567
East Asian	0.000273	0.000272
Finnish	0.00735	0.00733
European (Non-Finnish)	0.000972	0.000959
Middle Eastern	0.000273	0.000272
South Asian	0.000131	0.000131
Other	0.00262	0.00261

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine, and 7-methylguanine from the damaged DNA polymer formed by alkylation lesions.
• Pathway: Base excision repair - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;DNA Repair;Recognition and association of DNA glycosylase with site containing an affected purine;Cleavage of the damaged purine;Depurination;Base-Excision Repair, AP Site Formation;Resolution of Abasic Sites (AP sites);Base Excision Repair;Displacement of DNA glycosylase by APEX1;Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.418

Intolerance Scores

• loftool: 0.933
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.441
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpg
• Phenotype: limbs/digits/tail phenotype; immune system phenotype; neoplasm; endocrine/exocrine gland phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: base-excision repair;DNA dealkylation involved in DNA repair;depurination
• Cellular component: nucleoplasm;mitochondrial nucleoid
• Molecular function: damaged DNA binding;alkylbase DNA N-glycosylase activity;protein binding;DNA-3-methyladenine glycosylase activity;DNA N-glycosylase activity;DNA-7-methylguanine glycosylase activity;DNA-7-methyladenine glycosylase activity;DNA-3-methylguanine glycosylase activity