CPNE2

copine 2, the group of Copines

Basic information

Region (hg38): 16:57092583-57148369

Links

ENSG00000140848 ∙ NCBI:221184 ∙ OMIM:604206 ∙ HGNC:2315 ∙ Uniprot:Q96FN4 ∙ 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 CPNE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE2 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	0

Variants in CPNE2

This is a list of pathogenic ClinVar variants found in the CPNE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57110765-G-T		not specified	Uncertain significance (May 30, 2023)
16-57110777-C-T		not specified	Uncertain significance (May 03, 2023)
16-57110783-C-A		not specified	Uncertain significance (Dec 21, 2023)
16-57110789-C-T		not specified	Uncertain significance (Jul 05, 2023)
16-57110807-G-A		not specified	Uncertain significance (May 05, 2023)
16-57110813-G-A		not specified	Uncertain significance (Oct 12, 2021)
16-57110861-T-C		not specified	Uncertain significance (Dec 21, 2023)
16-57113291-G-A		not specified	Uncertain significance (Dec 12, 2023)
16-57113353-C-G		not specified	Uncertain significance (May 24, 2024)
16-57113387-G-A		not specified	Uncertain significance (Jan 07, 2022)
16-57113454-G-A		not specified	Uncertain significance (Aug 22, 2023)
16-57115523-C-G		not specified	Uncertain significance (Jul 25, 2023)
16-57115549-C-T		not specified	Uncertain significance (Jan 30, 2024)
16-57117499-G-A		not specified	Uncertain significance (Apr 14, 2022)
16-57117521-A-G		not specified	Uncertain significance (Jun 30, 2023)
16-57117526-G-A		not specified	Uncertain significance (Jan 10, 2023)
16-57119255-T-G		not specified	Uncertain significance (Jun 07, 2024)
16-57119262-T-A		not specified	Uncertain significance (Oct 06, 2021)
16-57121109-A-G		not specified	Uncertain significance (Aug 12, 2022)
16-57121115-A-G		not specified	Uncertain significance (Feb 03, 2022)
16-57121141-G-A		not specified	Uncertain significance (May 04, 2022)
16-57121177-C-G		not specified	Uncertain significance (Oct 26, 2021)
16-57121178-G-A		not specified	Uncertain significance (Dec 07, 2021)
16-57121190-C-T		not specified	Uncertain significance (Dec 20, 2023)
16-57123424-A-C		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE2	protein_coding	protein_coding	ENST00000535318	15	55430

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00130	0.999	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	264	344	0.767	0.0000209	3613
Missense in Polyphen		75	132.53	0.56591		1424
Synonymous	0.0179	146	146	0.998	0.0000101	1034
Loss of Function	3.47	11	32.3	0.341	0.00000185	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000879	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent phospholipid-binding protein that plays a role in calcium-mediated intracellular processes. Exhibits calcium-dependent cell membrane binding properties. {ECO:0000250|UniProtKB:P59108}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.349
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.199
• hipred: Y
• hipred_score: 0.639
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.825

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne2

Gene ontology

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