CPPED1

calcineurin like phosphoesterase domain containing 1

Basic information

Region (hg38): 16:12659798-12803887

Links

ENSG00000103381 ∙ NCBI:55313 ∙ OMIM:615603 ∙ HGNC:25632 ∙ Uniprot:Q9BRF8 ∙ 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 CPPED1 gene.

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPPED1 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in CPPED1

This is a list of pathogenic ClinVar variants found in the CPPED1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-12664959-C-T		not specified	Uncertain significance (Dec 06, 2021)
16-12664990-C-T		not specified	Uncertain significance (Dec 27, 2022)
16-12665024-G-C		not specified	Uncertain significance (Feb 12, 2024)
16-12665047-C-A		not specified	Uncertain significance (Oct 02, 2023)
16-12665074-C-T		not specified	Uncertain significance (Feb 27, 2024)
16-12665101-A-C		not specified	Uncertain significance (Aug 05, 2021)
16-12704627-C-T		not specified	Uncertain significance (Sep 01, 2021)
16-12704633-T-A		not specified	Uncertain significance (Jun 07, 2023)
16-12704697-G-T		not specified	Uncertain significance (Oct 05, 2023)
16-12704698-T-A		not specified	Uncertain significance (Aug 09, 2021)
16-12704702-T-C		not specified	Uncertain significance (Dec 11, 2023)
16-12704724-G-T		not specified	Uncertain significance (Oct 06, 2021)
16-12704756-G-A		not specified	Uncertain significance (Oct 10, 2023)
16-12704818-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-12704828-G-A		not specified	Uncertain significance (Dec 11, 2023)
16-12704929-T-A		not specified	Uncertain significance (Feb 05, 2024)
16-12704941-G-T		not specified	Uncertain significance (Jan 30, 2024)
16-12704987-C-A		not specified	Uncertain significance (Oct 05, 2023)
16-12704990-T-C		not specified	Uncertain significance (Feb 17, 2024)
16-12705010-C-T		not specified	Uncertain significance (Jul 25, 2023)
16-12705043-G-A		not specified	Uncertain significance (Jul 25, 2023)
16-12781247-T-C		not specified	Uncertain significance (Jun 12, 2023)
16-12781259-A-G		not specified	Uncertain significance (Oct 27, 2023)
16-12781296-C-T		not specified	Uncertain significance (Aug 17, 2021)
16-12781311-C-T		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPPED1	protein_coding	protein_coding	ENST00000381774	4	140956

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.32e-7	0.287	124749	0	46	124795	0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.956	232	194	1.19	0.0000121	2053
Missense in Polyphen		64	54.907	1.1656		591
Synonymous	-1.56	111	91.9	1.21	0.00000709	596
Loss of Function	0.404	11	12.5	0.877	6.24e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000669	0.000669
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000883
Middle Eastern	0.000167	0.000167
South Asian	0.000295	0.000294
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that dephosphorylates AKT family kinase specifically at 'Ser-473', blocking cell cycle progression and promoting cell apoptosis. May play an inhibitory role in glucose uptake by adipocytes. {ECO:0000269|PubMed:23799035, ECO:0000269|PubMed:23939394}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• loftool: 0.401
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.84

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.204
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.629

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpped1

Gene ontology

• Biological process: protein dephosphorylation;neutrophil degranulation
• Cellular component: extracellular region;cytosol;plasma membrane;azurophil granule lumen
• Molecular function: phosphoprotein phosphatase activity;metal ion binding