CPLX2

complexin 2

Basic information

Region (hg38): 5:175796309-175884021

Links

ENSG00000145920 ∙ NCBI:10814 ∙ OMIM:605033 ∙ HGNC:2310 ∙ Uniprot:Q6PUV4 ∙ 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 CPLX2 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLX2 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in CPLX2

This is a list of pathogenic ClinVar variants found in the CPLX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-175879990-T-C		not specified	Uncertain significance (Nov 27, 2023)
5-175880016-G-A		not specified	Uncertain significance (Jun 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPLX2	protein_coding	protein_coding	ENST00000359546	3	87711

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.526	0.459	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	47	80.3	0.585	0.00000442	868
Missense in Polyphen		15	37.131	0.40397		378
Synonymous	0.0525	33	33.4	0.988	0.00000209	228
Loss of Function	1.96	1	6.32	0.158	2.73e-7	82

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons. Positively regulates a late step in exocytosis of various cytoplasmic vesicles, such as synaptic vesicles and other secretory vesicles. Also involved in mast cell exocytosis (By similarity). {ECO:0000250|UniProtKB:P84086, ECO:0000250|UniProtKB:P84088}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Synaptic Vesicle Pathway (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.355
• hipred: Y
• hipred_score: 0.617
• ghis: 0.707

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cplx2
• 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: vesicle docking involved in exocytosis;nervous system development;synaptic vesicle exocytosis;regulation of exocytosis;cell differentiation;regulation of synaptic vesicle fusion to presynaptic active zone membrane;positive regulation of synaptic plasticity;mast cell degranulation;regulation of neurotransmitter secretion
• Cellular component: cytosol;dendrite;SNARE complex;mast cell granule;neuronal cell body;terminal bouton;calyx of Held;synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex;synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex;postsynapse;glutamatergic synapse
• Molecular function: SNARE binding;syntaxin-1 binding;calcium-dependent protein binding