PM20D2

protein-coding

peptidase M20 domain containing 2, the group of M20 metallopeptidases

Gene summary

Enables dipeptidase activity and identical protein binding activity. Acts upstream of or within proteolysis and regulation of protein metabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ACY1L2

MANE transcript

NM_001010853.3

Inheritance

—

ClinVar variants

U:78B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr6:89,146,055-89,165,565

External References & Databases

Ensembl (ENSG00000146281)

Transcript & Mutation Effects

hg38 • Region Span ~19.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PM20D2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010853.3. 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			3
missense			73 clinvar	3 clinvar		76
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	78	3	0	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010853.3	RefSeq	NP_001010853.1	7	MANE Select
ENST00000275072.5	Ensembl	ENSP00000275072.4	7	MANE Select
ENST00000879768.1	Ensembl	ENSP00000549827.1	4	Standard
ENST00000879768.2	Ensembl	ENSP00000549827.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
regulation of cellular protein metabolic process
folic acid catabolic process

Molecular Function

dipeptidase activity
para-aminobenzoyl-glutamate hydrolase activity

Cellular Component

nucleoplasm
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000275072
Coding exons: 7
Length: 19516
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 34
Defined: 125746
p: 0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.979	171	211	0.810	0.00000995	2761
Missense (PolyPhen)		38	60.19	0.63134		729
Synonymous	0.915	74	84.7	0.874	0.00000421	887
Loss of Function	1.59	9	15.8	0.569	6.65e-7	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.00033	0.00033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.102

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.239

Gene Damage Prediction

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