CADPS2

calcium dependent secretion activator 2, the group of Pleckstrin homology domain containing|C2 domain containing

Basic information

Region (hg38): 7:122318410-122886759

Links

ENSG00000081803 ∙ NCBI:93664 ∙ OMIM:609978 ∙ HGNC:16018 ∙ Uniprot:Q86UW7 ∙ 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 CADPS2 gene.

• Inborn genetic diseases (79 variants)
• not provided (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CADPS2 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				4	5	9
missense			44	5	3	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3		3
non coding			32	4	1	37
Total	0	0	76	13	9

Variants in CADPS2

This is a list of pathogenic ClinVar variants found in the CADPS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-122320353-T-G			Benign (Jan 09, 2019)
7-122325503-G-A			Likely benign (Oct 23, 2018)
7-122345638-C-T		not specified	Uncertain significance (Jul 15, 2021)
7-122345657-T-A		not specified	Uncertain significance (Dec 13, 2022)
7-122360793-C-T		not specified	Uncertain significance (Apr 07, 2023)
7-122360944-T-G		not specified	Uncertain significance (Oct 27, 2023)
7-122360968-C-T		not specified	Uncertain significance (Nov 10, 2022)
7-122379433-G-A		not specified	Uncertain significance (May 23, 2023)
7-122387040-C-G		not specified	Uncertain significance (Feb 06, 2023)
7-122387076-C-T		CADPS2-related disorder	Likely benign (Feb 01, 2022)
7-122388635-C-G		not specified	Uncertain significance (Feb 16, 2023)
7-122388696-A-T		not specified	Uncertain significance (Mar 17, 2023)
7-122388719-C-T			Benign (Dec 31, 2019)
7-122393222-C-T			Likely benign (Mar 01, 2024)
7-122393223-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-122393229-G-T		not specified	Uncertain significance (Jan 11, 2023)
7-122393451-G-C			Likely benign (Jun 23, 2018)
7-122393458-C-A		not specified	Uncertain significance (Feb 06, 2023)
7-122393490-C-T		not specified	Uncertain significance (Apr 13, 2022)
7-122393535-C-T		not specified	Uncertain significance (May 31, 2023)
7-122393555-T-C		not specified	Uncertain significance (Feb 22, 2023)
7-122407624-C-A		not specified	Uncertain significance (Nov 22, 2023)
7-122407677-T-C		not specified	Uncertain significance (Jul 20, 2022)
7-122416066-C-T		not specified	Uncertain significance (Aug 09, 2021)
7-122416138-T-C		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CADPS2	protein_coding	protein_coding	ENST00000449022	30	568333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.368	0.632	124642	0	37	124679	0.000148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	561	639	0.878	0.0000320	8445
Missense in Polyphen		128	183.71	0.69676		2391
Synonymous	0.570	222	233	0.953	0.0000120	2375
Loss of Function	6.03	16	70.7	0.226	0.00000358	918

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000212
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.000170	0.000167
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000198	0.000195
Middle Eastern	0.000170	0.000167
South Asian	0.0000342	0.0000327
Other	0.000187	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-binding protein involved in exocytosis of vesicles filled with neurotransmitters and neuropeptides. Probably acts upstream of fusion in the biogenesis or maintenance of mature secretory vesicles. Regulates neurotrophin release from granule cells leading to regulate cell differentiation and survival during cerebellar development. May specifically mediate the Ca(2+)- dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.02

Haploinsufficiency Scores

• pHI: 0.451
• hipred: Y
• hipred_score: 0.544
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cadps2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular response to starvation;protein transport;synaptic vesicle priming;positive regulation of exocytosis;dense core granule exocytosis
• Cellular component: nucleoplasm;cell junction;cytoplasmic vesicle membrane;presynaptic membrane;intracellular membrane-bounded organelle;postsynaptic membrane;parallel fiber to Purkinje cell synapse;glutamatergic synapse
• Molecular function: lipid binding;metal ion binding