CPNE9

copine family member 9, the group of Copines

Basic information

Region (hg38): 3:9703826-9729908

Links

ENSG00000144550 ∙ NCBI:151835 ∙ ∙ HGNC:24336 ∙ Uniprot:Q8IYJ1 ∙ 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 CPNE9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPNE9 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			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	0

Variants in CPNE9

This is a list of pathogenic ClinVar variants found in the CPNE9 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9704000-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-9704021-C-G		not specified	Uncertain significance (Jan 30, 2024)
3-9704022-G-A		not specified	Uncertain significance (Oct 06, 2022)
3-9704031-C-G		not specified	Uncertain significance (Sep 20, 2023)
3-9704031-C-T		not specified	Uncertain significance (Dec 04, 2024)
3-9704607-C-T		not specified	Uncertain significance (Nov 07, 2023)
3-9704617-G-C		not specified	Uncertain significance (Dec 16, 2022)
3-9706024-T-G		not specified	Uncertain significance (Sep 27, 2022)
3-9706054-G-A		not specified	Uncertain significance (Aug 28, 2024)
3-9712543-G-C		not specified	Uncertain significance (Feb 08, 2025)
3-9712561-G-A		not specified	Uncertain significance (Aug 14, 2024)
3-9712573-T-G		not specified	Uncertain significance (Feb 27, 2025)
3-9712746-T-C		not specified	Uncertain significance (Sep 27, 2021)
3-9712772-C-A		not specified	Uncertain significance (Mar 30, 2022)
3-9713003-G-A		not specified	Uncertain significance (Feb 22, 2024)
3-9713019-A-G		not specified	Uncertain significance (Dec 25, 2024)
3-9713063-A-G		not specified	Uncertain significance (Aug 12, 2024)
3-9714916-C-T		not specified	Uncertain significance (Aug 16, 2022)
3-9715300-T-C		not specified	Uncertain significance (Jul 26, 2024)
3-9715476-C-G		not specified	Uncertain significance (Dec 06, 2022)
3-9715486-G-A		not specified	Uncertain significance (Jan 08, 2025)
3-9715983-C-G		not specified	Uncertain significance (Jan 23, 2024)
3-9716011-C-T		not specified	Uncertain significance (Jul 31, 2024)
3-9717084-T-C		not specified	Uncertain significance (Jun 25, 2024)
3-9718071-A-T		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPNE9	protein_coding	protein_coding	ENST00000383832	21	26102

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.49e-8	0.999	125365	0	50	125415	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	240	327	0.733	0.0000178	3616
Missense in Polyphen		77	139.65	0.55138		1579
Synonymous	-0.0548	127	126	1.01	0.00000694	1057
Loss of Function	3.01	19	39.4	0.482	0.00000231	408

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000619	0.000594
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000282	0.000273
Finnish	0.0000482	0.0000463
European (Non-Finnish)	0.000152	0.000150
Middle Eastern	0.000282	0.000273
South Asian	0.000296	0.000294
Other	0.000342	0.000328

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}.

Intolerance Scores

• loftool: 0.608
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.693
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cpne9

Gene ontology

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