MPPED2

protein-coding

metallophosphoesterase domain containing 2

Gene summary

Predicted to enable cyclic-nucleotide phosphodiesterase activity; manganese ion binding activity; and purine ribonucleotide binding activity. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C11orf8

MANE transcript

NM_001584.3

Inheritance

—

ClinVar variants

U:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr11:30,384,493-30,586,872

External References & Databases

Ensembl (ENSG00000066382)

Transcript & Mutation Effects

hg38 • Region Span ~202.4 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 MPPED2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001584.3. 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			1 clinvar			1
missense			14 clinvar			14
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	17	0	0	17

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001584.3	RefSeq	NP_001575.1	6	MANE Select
ENST00000358117.10	Ensembl	ENSP00000350833.4	6	MANE Select
NM_001145399.3	RefSeq	NP_001138871.1	6	Standard
NM_001377952.1	RefSeq	NP_001364881.1	6	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
mpped2	Danio rerio	Structure: heart Quality: edematous abnormal

Gene / Model

Organism

Observed Phenotype

mpped2

Danio rerio

Structure: heart

Quality: edematous

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nervous system development

Molecular Function

protein binding
hydrolase activity
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358117
Coding exons: 6
Length: 202380
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125710
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.00	98	172	0.571	0.00000920	1933
Missense (PolyPhen)		34	73.74	0.46108		789
Synonymous	0.600	64	70.4	0.909	0.00000441	569
Loss of Function	3.59	0	15.0	0.00	7.86e-7	164

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Displays low metallophosphoesterase activity (in vitro). May play a role in the development of the nervous system (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.0966
RVIS EVS: -0.23
RVIS percentile EVS: 36.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.427

Gene Damage Prediction

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