CPNE7

copine 7, the group of Copines

Basic information

Region (hg38): 16:89575758-89597246

Links

ENSG00000178773 ∙ NCBI:27132 ∙ OMIM:605689 ∙ HGNC:2320 ∙ Uniprot:Q9UBL6 ∙ 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 CPNE7 gene.

• not_specified (143 variants)
• not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153636.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			122	5		127
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	122	7	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE7	protein_coding	protein_coding	ENST00000268720	17	21479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-24	0.000310	125682	0	57	125739	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.978	444	390	1.14	0.0000259	4077
Missense in Polyphen		182	157.89	1.1527		1632
Synonymous	-3.43	237	179	1.33	0.0000139	1239
Loss of Function	-0.223	35	33.6	1.04	0.00000167	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000531	0.000522
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000332	0.000317
Middle Eastern	0.000167	0.000163
South Asian	0.000275	0.000261
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. {ECO:0000250|UniProtKB:Q99829}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Intolerance Scores

• loftool: 0.859
• rvis_EVS: -1.34
• rvis_percentile_EVS: 4.65

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.275
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne7

Gene ontology

• Biological process: lipid metabolic process;glycerophospholipid biosynthetic process;cellular response to calcium ion
• Cellular component: nucleus;cytoplasm;plasma membrane;extracellular exosome
• Molecular function: transporter activity;protein binding;calcium-dependent phospholipid binding