MPPED2

metallophosphoesterase domain containing 2

Basic information

Region (hg38): 11:30384493-30586872

Previous symbols: [ "C11orf8" ]

Links

ENSG00000066382 ∙ NCBI:744 ∙ OMIM:600911 ∙ HGNC:1180 ∙ Uniprot:Q15777 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MPPED2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPPED2 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in MPPED2

This is a list of pathogenic ClinVar variants found in the MPPED2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-30411556-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-30417550-A-G		not specified	Uncertain significance (Mar 18, 2024)
11-30417553-C-T		not specified	Uncertain significance (Aug 17, 2021)
11-30536140-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPPED2	protein_coding	protein_coding	ENST00000358117	6	202380

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00651	125709	0	1	125710	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.00	98	172	0.571	0.00000920	1933
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0662
• hipred: Y
• hipred_score: 0.774
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.427

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpped2

Zebrafish Information Network

• Gene name: mpped2
• Affected structure: heart
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: nervous system development
• Molecular function: protein binding;hydrolase activity;metal ion binding