MPPED1

metallophosphoesterase domain containing 1

Basic information

Region (hg38): 22:43411196-43507848

Previous symbols: [ "C22orf1" ]

Links

ENSG00000186732 ∙ NCBI:758 ∙ OMIM:602112 ∙ HGNC:1306 ∙ Uniprot:O15442 ∙ 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 MPPED1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPPED1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in MPPED1

This is a list of pathogenic ClinVar variants found in the MPPED1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43424996-C-G		not specified	Uncertain significance (May 13, 2024)
22-43425006-T-G		not specified	Uncertain significance (Jan 27, 2022)
22-43425049-G-A		not specified	Uncertain significance (Aug 30, 2021)
22-43425079-G-A		not specified	Uncertain significance (May 29, 2024)
22-43425116-T-C		not specified	Uncertain significance (Dec 13, 2022)
22-43425128-A-G		not specified	Uncertain significance (Jun 17, 2024)
22-43425143-A-G		not specified	Uncertain significance (Feb 27, 2024)
22-43435120-C-A		not specified	Uncertain significance (Dec 15, 2023)
22-43435150-T-G		not specified	Uncertain significance (Dec 21, 2022)
22-43474744-C-T		not specified	Uncertain significance (Oct 12, 2022)
22-43474930-G-A		not specified	Uncertain significance (Jan 02, 2024)
22-43498317-G-A		not specified	Uncertain significance (May 30, 2023)
22-43502644-G-T		not specified	Uncertain significance (Dec 20, 2021)
22-43502718-G-A		not specified	Uncertain significance (Sep 26, 2023)
22-43505522-C-T		not specified	Uncertain significance (Apr 12, 2024)
22-43505570-T-C		not specified	Uncertain significance (May 29, 2024)
22-43505576-C-T		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPPED1	protein_coding	protein_coding	ENST00000417669	6	96527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00198	0.979	124862	0	9	124871	0.0000360

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.60	113	222	0.509	0.0000150	2132
Missense in Polyphen		34	76.607	0.44382		719
Synonymous	0.607	94	102	0.924	0.00000780	643
Loss of Function	2.06	7	15.8	0.442	7.56e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000110
Finnish	0.00	0.00
European (Non-Finnish)	0.0000497	0.0000442
Middle Eastern	0.000112	0.000110
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have metallophosphoesterase activity (in vitro). {ECO:0000250}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.212
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.538
• ghis: 0.682

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpped1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function;hydrolase activity