CLSTN3

calsyntenin 3, the group of Cadherin related

Basic information

Region (hg38): 12:7129698-7158945

Links

ENSG00000139182 ∙ NCBI:9746 ∙ OMIM:611324 ∙ HGNC:18371 ∙ Uniprot:Q9BQT9 ∙ 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 CLSTN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLSTN3 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				3	1	4
missense			80		2	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	80	3	3

Variants in CLSTN3

This is a list of pathogenic ClinVar variants found in the CLSTN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7130691-G-T			Benign (Oct 01, 2024)
12-7133120-A-G		not specified	Uncertain significance (Feb 05, 2024)
12-7133132-C-T		not specified	Uncertain significance (Dec 06, 2021)
12-7133137-C-T		not specified	Uncertain significance (Aug 04, 2024)
12-7133629-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-7133639-C-T		not specified	Uncertain significance (Sep 27, 2021)
12-7133640-G-A			Likely benign (Mar 01, 2022)
12-7133671-C-G		not specified	Uncertain significance (Dec 20, 2023)
12-7133731-G-A		not specified	Uncertain significance (Jan 31, 2023)
12-7133753-C-G		not specified	Uncertain significance (Mar 10, 2025)
12-7135338-A-T		not specified	Uncertain significance (Dec 03, 2021)
12-7135394-C-T		not specified	Uncertain significance (Dec 12, 2023)
12-7135400-G-A		not specified	Uncertain significance (Nov 24, 2024)
12-7135427-C-T		not specified	Uncertain significance (Mar 15, 2024)
12-7135505-C-A		not specified	Uncertain significance (Jul 12, 2022)
12-7135524-T-C		not specified	Uncertain significance (Mar 25, 2024)
12-7135810-T-C		Autism spectrum disorder	association (-)
12-7135844-G-C		not specified	Uncertain significance (Sep 30, 2021)
12-7135861-C-T		not specified	Uncertain significance (Sep 06, 2022)
12-7136206-G-T		not specified	Uncertain significance (Aug 22, 2023)
12-7136219-G-T		not specified	Uncertain significance (Mar 05, 2025)
12-7136240-T-C			Benign (Dec 01, 2022)
12-7136259-C-T		not specified	Uncertain significance (Sep 26, 2023)
12-7136265-A-G		not specified	Uncertain significance (May 23, 2024)
12-7136374-C-T		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLSTN3	protein_coding	protein_coding	ENST00000266546	18	29248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.970	0.0298	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	487	589	0.826	0.0000366	6244
Missense in Polyphen		75	130.35	0.57539		1478
Synonymous	-0.166	246	243	1.01	0.0000155	1910
Loss of Function	4.98	7	41.7	0.168	0.00000195	481

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000803	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.364
• rvis_EVS: -1.65
• rvis_percentile_EVS: 2.76

Haploinsufficiency Scores

• pHI: 0.359
• hipred: Y
• hipred_score: 0.654
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.293

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clstn3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); skeleton phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of cell growth;homophilic cell adhesion via plasma membrane adhesion molecules;synapse assembly;synaptic transmission, glutamatergic;positive regulation of synaptic transmission;synaptic transmission, GABAergic;positive regulation of synapse assembly;positive regulation of protein localization to synapse;regulation of presynapse assembly
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cell surface;protein-containing complex;postsynaptic membrane;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic density membrane
• Molecular function: calcium ion binding