MPG

protein-coding

N-methylpurine DNA glycosylase, the group of DNA glycosylases

Gene summary

Enables DNA binding activity. Predicted to be involved in base-excision repair. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001015052.3

Inheritance

—

ClinVar variants

U:69B:6

Top phenotype

MPG-related condition

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr16:77,007-85,851

External References & Databases

Ensembl (ENSG00000103152)

Transcript & Mutation Effects

hg38 • Region Span ~8.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MPG variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 6

MPG-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001015052.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense			66 clinvar	1 clinvar		67
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	69	4	2	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001015052.3	RefSeq	NP_001015052.1	4	MANE Select
ENST00000356432.8	Ensembl	ENSP00000348809.4	4	MANE Select
NM_001015054.3	RefSeq	NP_001015054.1	3	Standard
NM_002434.4	RefSeq	NP_002425.2	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

base-excision repair
DNA dealkylation involved in DNA repair
depurination

Molecular Function

damaged DNA binding
alkylbase DNA N-glycosylase activity
protein binding
DNA-3-methyladenine glycosylase activity
DNA N-glycosylase activity

Cellular Component

nucleoplasm
mitochondrial nucleoid

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000219431
Coding exons: 4
Length: 8847
Individuals with no LoFs: 125350
Homozygous LoFs: 1
Heterozygous LoFs: 383
Defined: 125734
p: 0.00153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.489	220	201	1.10	0.0000137	1883
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.00076	0.00075	rare
Ashkenazi Jewish	0.0057	0.0057	notable
East Asian	0.00027	0.00027	rare
Finnish	0.0074	0.0073	notable
European (Non-Finnish)	0.00097	0.00096	rare
South Asian	0.00013	0.00013	rare
Other	0.0026	0.0026	notable

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.418

Intolerance Scores

LoFtool: 0.933
RVIS EVS: -0.84
RVIS percentile EVS: 11.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.820

Gene Damage Prediction

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