CADPS

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

Basic information

Region (hg38): 3:62398345-62875416

Links

ENSG00000163618 ∙ NCBI:8618 ∙ OMIM:604667 ∙ HGNC:1426 ∙ Uniprot:Q9ULU8 ∙ 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 CADPS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CADPS 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				17	3	20
missense			49	3	1	53
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	3	2	6
non coding				2		2
Total	0	0	52	22	4

Variants in CADPS

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

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

Position	Type	Phenotype	Significance	ClinVar
3-62399469-T-G		not specified	Uncertain significance (Apr 19, 2024)
3-62399594-G-A		CADPS-related disorder	Likely benign (Nov 04, 2019)
3-62403100-G-A		not specified	Uncertain significance (Feb 27, 2023)
3-62403141-C-T		CADPS-related disorder	Likely benign (Jun 25, 2019)
3-62403156-GA-G		CADPS-related disorder	Uncertain significance (Sep 26, 2022)
3-62403161-C-T		not specified	Uncertain significance (Jun 21, 2021)
3-62403173-T-C		CADPS-related disorder	Likely benign (Apr 15, 2022)
3-62403183-T-C		CADPS-related disorder	Uncertain significance (Mar 21, 2023)
3-62438196-C-A		CADPS-related disorder • not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
3-62445781-T-C		not specified	Uncertain significance (Oct 26, 2021)
3-62465410-C-A		CADPS-related disorder	Uncertain significance (Apr 26, 2023)
3-62465447-C-T		not specified	Uncertain significance (Jun 29, 2022)
3-62466368-T-C		not specified	Uncertain significance (Dec 01, 2022)
3-62466394-AT-A			Uncertain significance (May 01, 2017)
3-62474166-T-C		CADPS-related disorder	Likely benign (Apr 09, 2019)
3-62474171-A-C		CADPS-related disorder	Uncertain significance (Jan 03, 2024)
3-62474264-C-T		not specified	Uncertain significance (Mar 04, 2024)
3-62474310-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-62481726-G-A		not specified	Uncertain significance (Jun 30, 2023)
3-62481752-C-T			Likely benign (Apr 16, 2018)
3-62481759-G-A		not specified	Uncertain significance (May 03, 2023)
3-62481846-T-A		CADPS-related disorder	Likely benign (Dec 26, 2019)
3-62492298-C-G		not specified	Uncertain significance (Dec 13, 2023)
3-62492298-C-T		not specified	Uncertain significance (Dec 14, 2023)
3-62492310-T-C		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CADPS	protein_coding	protein_coding	ENST00000383710	30	477033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000147	1.00	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.10	525	767	0.685	0.0000446	8911
Missense in Polyphen		17	34.822	0.48819		321
Synonymous	-1.44	319	288	1.11	0.0000173	2521
Loss of Function	5.64	24	77.6	0.309	0.00000432	862

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000154
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000491	0.000489

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 catecholamine loading of DCVs. May specifically mediate the Ca(2+)-dependent exocytosis of large dense-core vesicles (DCVs) and other dense-core vesicles by acting as a PtdIns(4,5)P2-binding protein that acts at prefusion step following ATP-dependent priming and participates in DCVs-membrane fusion. However, it may also participate in small clear synaptic vesicles (SVs) exocytosis and it is unclear whether its function is related to Ca(2+) triggering (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.384
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.63

Haploinsufficiency Scores

• pHI: 0.465
• hipred: Y
• hipred_score: 0.658
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cadps
• Phenotype: 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); respiratory system phenotype; 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); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: exocytosis;protein transport;synaptic vesicle exocytosis;dense core granule exocytosis
• Cellular component: cytosol;cell junction;cytoplasmic vesicle membrane;presynapse
• Molecular function: protein binding;lipid binding;protein kinase binding;metal ion binding