CLSTN2

calsyntenin 2, the group of Cadherin related

Basic information

Region (hg38): 3:139935184-140577397

Links

ENSG00000158258 ∙ NCBI:64084 ∙ OMIM:611323 ∙ HGNC:17448 ∙ Uniprot:Q9H4D0 ∙ 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 CLSTN2 gene.

• Inborn genetic diseases (43 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLSTN2 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				4	3	7
missense			42	4		46
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	42	8	4

Variants in CLSTN2

This is a list of pathogenic ClinVar variants found in the CLSTN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-139935399-G-T		not specified	Uncertain significance (Aug 20, 2023)
3-139935417-C-A		not specified	Uncertain significance (Aug 22, 2023)
3-139935441-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-139935442-G-A		not specified	Uncertain significance (Apr 12, 2022)
3-139935450-G-T		not specified	Uncertain significance (Jun 02, 2023)
3-140176047-A-G		not specified	Uncertain significance (Mar 08, 2024)
3-140403621-T-G			Benign (Dec 31, 2019)
3-140403710-G-A		not specified	Uncertain significance (Nov 09, 2023)
3-140403768-C-A			Benign (Jul 05, 2018)
3-140403775-T-A		not specified	Uncertain significance (Oct 26, 2022)
3-140403787-G-A		not specified	Uncertain significance (Mar 11, 2024)
3-140403798-C-T			Likely benign (Jul 31, 2018)
3-140404730-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-140404739-G-C		not specified	Uncertain significance (Dec 12, 2023)
3-140421148-C-A		not specified	Uncertain significance (Feb 13, 2024)
3-140421153-C-G		not specified	Uncertain significance (Aug 22, 2023)
3-140421236-A-G		not specified	Uncertain significance (Dec 15, 2023)
3-140448554-G-A		not specified	Uncertain significance (Nov 12, 2021)
3-140448581-C-T		not specified	Uncertain significance (Nov 20, 2023)
3-140448605-G-A		not specified	Uncertain significance (Sep 26, 2023)
3-140448623-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-140448648-T-A			Likely benign (Jul 01, 2022)
3-140448666-G-A		not specified	Uncertain significance (Nov 03, 2023)
3-140459568-A-G		not specified	Uncertain significance (Nov 15, 2021)
3-140459622-G-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLSTN2	protein_coding	protein_coding	ENST00000458420	17	642213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000352	1.00	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.680	511	556	0.919	0.0000324	6329
Missense in Polyphen		117	144.26	0.81104		1611
Synonymous	-1.04	232	213	1.09	0.0000134	1802
Loss of Function	3.67	17	42.9	0.396	0.00000193	526

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000884	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate calcium-mediated postsynaptic signals. {ECO:0000250}.

Recessive Scores

• pRec: 0.265

Intolerance Scores

• loftool: 0.513
• rvis_EVS: -0.43
• rvis_percentile_EVS: 24.72

Haploinsufficiency Scores

• pHI: 0.479
• hipred: Y
• hipred_score: 0.544
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clstn2
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;positive regulation of synaptic transmission;positive regulation of synapse assembly
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cell surface;postsynaptic membrane;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: calcium ion binding