CPLX4

complexin 4

Basic information

Region (hg38): 18:59275155-59318649

Links

ENSG00000166569 ∙ NCBI:339302 ∙ OMIM:609586 ∙ HGNC:24330 ∙ Uniprot:Q7Z7G2 ∙ 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 CPLX4 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPLX4 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in CPLX4

This is a list of pathogenic ClinVar variants found in the CPLX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-59296826-C-T		not specified	Uncertain significance (Jul 19, 2023)
18-59318306-T-C		not specified	Uncertain significance (Jun 22, 2021)
18-59318429-G-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPLX4	protein_coding	protein_coding	ENST00000299721	3	43494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000136	0.424	125730	0	13	125743	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0588	83	84.5	0.982	0.00000395	1093
Missense in Polyphen		26	30.4	0.85525		393
Synonymous	0.219	25	26.4	0.946	0.00000131	255
Loss of Function	0.182	6	6.50	0.923	2.73e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000105	0.0000980
Other	0.000164	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) (Consensus)

Recessive Scores

• pRec: 0.0964

Intolerance Scores

• loftool: 0.470
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.457
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cplx4
• Phenotype: 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)

Zebrafish Information Network

• Gene name: cplx4a
• Affected structure: retinal cone cell
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: synaptic vesicle exocytosis;regulation of neurotransmitter secretion
• Cellular component: cell junction;SNARE complex;terminal bouton
• Molecular function: SNARE binding;syntaxin binding