CPED1

cadherin like and PC-esterase domain containing 1

Basic information

Region (hg38): 7:120988696-121297442

Previous symbols: [ "C7orf58" ]

Links

ENSG00000106034 ∙ NCBI:79974 ∙ ∙ HGNC:26159 ∙ Uniprot:A4D0V7 ∙ 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 CPED1 gene.

• Inborn genetic diseases (45 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPED1 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				2	3	5
missense			42	5	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	43	7	4

Variants in CPED1

This is a list of pathogenic ClinVar variants found in the CPED1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-120989625-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-120989644-C-T		not specified	Likely benign (May 18, 2023)
7-120989752-C-G		not specified	Uncertain significance (Jun 16, 2023)
7-120989832-T-A		not specified	Uncertain significance (Jun 13, 2023)
7-120989862-A-G			Likely benign (Dec 01, 2022)
7-121015669-A-G		not specified	Uncertain significance (Aug 12, 2021)
7-121015679-G-A		not specified	Likely benign (Apr 07, 2022)
7-121015705-G-A		not specified	Uncertain significance (Nov 01, 2022)
7-121015713-A-G		not specified	Likely benign (Mar 07, 2024)
7-121015713-A-T		not specified	Uncertain significance (Jun 12, 2023)
7-121015753-A-C		not specified	Uncertain significance (Feb 02, 2024)
7-121015773-A-G		not specified	Uncertain significance (Jan 27, 2022)
7-121015789-C-T		not specified	Uncertain significance (Jul 09, 2021)
7-121015831-C-T			Likely benign (Jun 08, 2018)
7-121015835-G-A			Benign (Jul 23, 2018)
7-121046892-C-G		not specified	Uncertain significance (May 18, 2023)
7-121046917-G-T		not specified	Uncertain significance (Oct 26, 2022)
7-121046938-A-T		not specified	Uncertain significance (Aug 30, 2022)
7-121064245-G-T		not specified	Likely benign (May 31, 2023)
7-121097723-C-G		not specified	Uncertain significance (Aug 08, 2023)
7-121097741-G-A		not specified	Uncertain significance (Mar 07, 2023)
7-121097807-C-G		not specified	Uncertain significance (Jan 23, 2024)
7-121099934-C-T		not specified	Uncertain significance (Jun 29, 2023)
7-121100030-G-A		not specified	Uncertain significance (Dec 02, 2022)
7-121100045-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPED1	protein_coding	protein_coding	ENST00000310396	22	308768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.87e-24	0.0677	125543	0	205	125748	0.000815

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00125	527	527	1.00	0.0000260	6722
Missense in Polyphen		129	156.28	0.82545		2043
Synonymous	-1.13	215	195	1.10	0.0000103	1914
Loss of Function	1.56	44	56.7	0.776	0.00000285	680

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00265	0.00264
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.000329	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000810	0.000800
Middle Eastern	0.000329	0.000326
South Asian	0.00149	0.00147
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0845

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.35

Haploinsufficiency Scores

• pHI: 0.0572
• hipred: N
• hipred_score: 0.123
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cped1

Gene ontology

• Cellular component: endoplasmic reticulum