CLSTN1

calsyntenin 1, the group of Cadherin related

Basic information

Region (hg38): 1:9728926-9823984

Links

ENSG00000171603 ∙ NCBI:22883 ∙ OMIM:611321 ∙ HGNC:17447 ∙ Uniprot:O94985 ∙ 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 CLSTN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLSTN1 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				2	2	4
missense			52	4	1	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	52	7	3

Variants in CLSTN1

This is a list of pathogenic ClinVar variants found in the CLSTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-9730521-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-9730548-T-C		not specified	Uncertain significance (Nov 26, 2024)
1-9730601-C-G			Likely benign (Aug 01, 2023)
1-9730602-T-C		not specified	Uncertain significance (Aug 30, 2022)
1-9730639-C-T		not specified	Uncertain significance (Jun 23, 2023)
1-9731222-G-C		not specified	Uncertain significance (Mar 13, 2023)
1-9731268-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-9731282-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-9731297-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-9731778-T-C		not specified	Likely benign (Nov 14, 2023)
1-9731880-G-A		not specified	Uncertain significance (Aug 30, 2022)
1-9733392-T-C			Likely benign (Mar 06, 2018)
1-9733457-T-G		not specified	Uncertain significance (Mar 29, 2023)
1-9733477-G-T		not specified	Uncertain significance (Jun 29, 2023)
1-9733478-A-T		not specified	Uncertain significance (Jun 29, 2023)
1-9733525-T-C		not specified	Uncertain significance (Nov 03, 2023)
1-9733535-T-C		not specified	Uncertain significance (May 04, 2022)
1-9734020-G-C		not specified	Uncertain significance (Jan 23, 2024)
1-9734028-C-T		not specified	Uncertain significance (Sep 10, 2024)
1-9734113-C-T		not specified	Uncertain significance (Aug 12, 2024)
1-9734122-C-T		not specified	Uncertain significance (Nov 27, 2024)
1-9734992-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-9735085-C-T		not specified	Uncertain significance (May 26, 2023)
1-9735103-T-C		not specified	Uncertain significance (Aug 28, 2024)
1-9735139-G-C		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLSTN1	protein_coding	protein_coding	ENST00000377298	19	95501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0224	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	525	595	0.882	0.0000384	6483
Missense in Polyphen		181	230.2	0.78626		2471
Synonymous	-0.807	280	263	1.06	0.0000206	1886
Loss of Function	5.26	8	46.9	0.171	0.00000235	547

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces KLC1 association with vesicles and functions as a cargo in axonal anterograde transport. 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. In complex with APBA2 and C99, a C-terminal APP fragment, abolishes C99 interaction with PSEN1 and thus APP C99 cleavage by gamma-secretase, most probably through stabilization of the direct interaction between APBA2 and APP. The intracellular fragment AlcICD suppresses APBB1-dependent transactivation stimulated by APP C-terminal intracellular fragment (AICD), most probably by competing with AICD for APBB1- binding. May modulate calcium-mediated postsynaptic signals (By similarity). {ECO:0000250, ECO:0000269|PubMed:12972431}.
• Pathway: Splicing factor NOVA regulated synaptic proteins (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.289
• rvis_EVS: -1.05
• rvis_percentile_EVS: 7.6

Haploinsufficiency Scores

• pHI: 0.638
• hipred: Y
• hipred_score: 0.708
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.814

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clstn1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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: clstn1
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: regulation of cell growth;cell adhesion;homophilic cell adhesion via plasma membrane adhesion molecules;positive regulation of synaptic transmission;positive regulation of synapse assembly;regulation of synapse maturation;neurotransmitter receptor transport to postsynaptic membrane;vesicle-mediated transport in synapse
• Cellular component: Golgi membrane;extracellular region;nucleus;endoplasmic reticulum membrane;cell surface;cell junction;postsynaptic membrane;postsynaptic endosome;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic density membrane;integral component of spine apparatus membrane
• Molecular function: amyloid-beta binding;calcium ion binding;protein binding;kinesin binding;X11-like protein binding