CPLX3

complexin 3

Basic information

Region (hg38): 15:74826627-74831802

Links

ENSG00000213578

∙ NCBI:594855 ∙ OMIM:609585 ∙ HGNC:27652 ∙ Uniprot:Q8WVH0 ∙ 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 CPLX3 gene.

not_specified (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLX3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001030005.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPLX3	protein_coding	protein_coding	ENST00000395018	3	5254

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.240	0.731	125683	0	13	125696	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	81	95.1	0.852	0.00000541	1025
Missense in Polyphen		28	36.288	0.77161		410
Synonymous	0.310	35	37.4	0.935	0.00000209	295
Loss of Function	1.84	2	7.39	0.271	3.98e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000943	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.000393	0.000359
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Positively regulates a late step in synaptic vesicle exocytosis. {ECO:0000250}.;
Pathway: Synaptic vesicle cycle - Homo sapiens (human);Synaptic Vesicle Pathway (Consensus)

Intolerance Scores

loftool: 0.246
rvis_EVS: 0.01
rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

pHI: 0.216
hipred: N
hipred_score: 0.380
ghis: 0.465

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.614

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cplx3
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); vision/eye 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);

Gene ontology

Biological process: synaptic vesicle exocytosis;insulin secretion;regulation of synaptic vesicle fusion to presynaptic active zone membrane;regulation of neurotransmitter secretion
Cellular component: cytosol;cell junction;SNARE complex;terminal bouton;photoreceptor ribbon synapse;anchored component of synaptic vesicle membrane;anchored component of presynaptic active zone membrane
Molecular function: SNARE binding;neurotransmitter transporter activity;syntaxin binding