CPNE5

copine 5, the group of Copines

Basic information

Region (hg38): 6:36740774-36839444

Links

ENSG00000124772 ∙ NCBI:57699 ∙ OMIM:604209 ∙ HGNC:2318 ∙ Uniprot:Q9HCH3 ∙ 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 CPNE5 gene.

• Inborn genetic diseases (20 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE5 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					3	3
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	0	20	0	5

Variants in CPNE5

This is a list of pathogenic ClinVar variants found in the CPNE5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-36742290-G-T		not specified	Uncertain significance (Jan 26, 2023)
6-36742292-C-A			Benign (Jun 11, 2018)
6-36742302-G-A		not specified	Uncertain significance (Jan 19, 2024)
6-36742306-G-A		not specified	Uncertain significance (Sep 14, 2021)
6-36742320-G-A		not specified	Uncertain significance (Oct 20, 2021)
6-36742324-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-36742353-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-36743708-G-T		not specified	Uncertain significance (Jul 11, 2023)
6-36743739-C-T		not specified	Uncertain significance (Jul 05, 2023)
6-36744269-G-T		not specified	Uncertain significance (Aug 11, 2022)
6-36745147-A-C			Benign (Jul 07, 2018)
6-36745418-T-C		not specified	Uncertain significance (Aug 29, 2022)
6-36745445-C-T		not specified	Uncertain significance (Dec 28, 2023)
6-36745446-G-A		not specified	Uncertain significance (Jan 17, 2023)
6-36745455-G-A		not specified	Uncertain significance (Mar 21, 2023)
6-36745524-C-T			Benign (Apr 04, 2018)
6-36748256-T-C		not specified	Uncertain significance (Nov 15, 2021)
6-36756271-T-C		not specified	Uncertain significance (Sep 14, 2022)
6-36762945-C-T		not specified	Uncertain significance (Dec 27, 2022)
6-36765374-G-T		not specified	Uncertain significance (May 23, 2023)
6-36774965-C-T		not specified	Uncertain significance (Nov 03, 2023)
6-36774990-C-T			Benign (Apr 04, 2018)
6-36778893-T-C		not specified	Uncertain significance (Jul 30, 2023)
6-36778933-C-T		not specified	Uncertain significance (Jan 10, 2022)
6-36792051-C-T			Benign (Feb 25, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE5	protein_coding	protein_coding	ENST00000244751	21	99227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000378	1.00	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.72	234	384	0.609	0.0000248	3889
Missense in Polyphen		78	174.03	0.44819		1779
Synonymous	0.611	152	162	0.939	0.0000120	1117
Loss of Function	3.74	13	37.8	0.344	0.00000218	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000621	0.0000544
Finnish	0.0000942	0.0000924
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.0000621	0.0000544
South Asian	0.000133	0.000131
Other	0.000186	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000250|UniProtKB:Q99829, ECO:0000269|PubMed:23999003}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.569
• rvis_EVS: -1
• rvis_percentile_EVS: 8.37

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.623
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.289

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne5
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cellular response to calcium ion;positive regulation of dendrite extension
• Cellular component: plasma membrane;neuron projection;perikaryon;extracellular exosome
• Molecular function: molecular_function;calcium-dependent phospholipid binding