CSPG5

chondroitin sulfate proteoglycan 5

Basic information

Region (hg38): 3:47562238-47580792

Links

ENSG00000114646 ∙ NCBI:10675 ∙ OMIM:606775 ∙ HGNC:2467 ∙ Uniprot:O95196 ∙ 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 CSPG5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSPG5 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				1	1	2
missense			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	1

Variants in CSPG5

This is a list of pathogenic ClinVar variants found in the CSPG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-47562647-C-T		not specified	Uncertain significance (May 01, 2024)
3-47562688-A-T		not specified	Uncertain significance (Jun 27, 2022)
3-47569090-T-C		not specified	Uncertain significance (Mar 07, 2024)
3-47569106-G-A		not specified	Uncertain significance (Aug 17, 2022)
3-47569114-G-A		not specified	Uncertain significance (Sep 11, 2024)
3-47569126-C-A		not specified	Uncertain significance (Nov 18, 2023)
3-47569180-G-C		not specified	Uncertain significance (Jun 27, 2023)
3-47569220-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-47572695-C-T		not specified	Uncertain significance (Nov 15, 2021)
3-47572696-G-A		not specified	Uncertain significance (Dec 16, 2022)
3-47572749-G-A		not specified	Uncertain significance (Feb 15, 2023)
3-47572774-C-T		not specified	Uncertain significance (Oct 19, 2024)
3-47572836-C-T		not specified	Uncertain significance (May 05, 2023)
3-47572863-T-G		not specified	Uncertain significance (Apr 07, 2022)
3-47572866-G-A		not specified	Uncertain significance (Apr 05, 2023)
3-47576888-A-G		not specified	Uncertain significance (Jan 23, 2024)
3-47576947-C-A		not specified	Uncertain significance (Apr 17, 2024)
3-47576996-C-T		not specified	Uncertain significance (Jun 24, 2022)
3-47577071-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-47577082-T-C		not specified	Uncertain significance (Nov 18, 2023)
3-47577101-G-C		not specified	Uncertain significance (May 26, 2022)
3-47577103-C-T		not specified	Uncertain significance (Mar 16, 2024)
3-47577189-C-G		not specified	Uncertain significance (Jan 26, 2022)
3-47577263-C-T		not specified	Uncertain significance (Mar 22, 2023)
3-47577294-C-G		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSPG5	protein_coding	protein_coding	ENST00000383738	5	18554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0562	0.940	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	251	318	0.788	0.0000180	3637
Missense in Polyphen		87	139.05	0.62565		1546
Synonymous	1.04	124	140	0.888	0.00000883	1193
Loss of Function	2.56	5	16.1	0.311	6.84e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000591	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.0000591	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a growth and differentiation factor involved in neuritogenesis. May induce ERBB3 activation. {ECO:0000269|PubMed:15358134}.
• Pathway: Metabolism of carbohydrates;A tetrasaccharide linker sequence is required for GAG synthesis;Heparan sulfate/heparin (HS-GAG) metabolism;Chondroitin sulfate biosynthesis;Dermatan sulfate biosynthesis;Chondroitin sulfate/dermatan sulfate metabolism;Glycosaminoglycan metabolism;Metabolism (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.368
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.472
• hipred: Y
• hipred_score: 0.622
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.406

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cspg5
• 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)

Gene ontology

• Biological process: nervous system development;regulation of signaling receptor activity;cell differentiation;chondroitin sulfate biosynthetic process;chondroitin sulfate catabolic process;dermatan sulfate biosynthetic process;regulation of growth;intracellular transport;trans-synaptic signaling, modulating synaptic transmission;regulation of synaptic vesicle exocytosis
• Cellular component: Golgi membrane;extracellular region;endoplasmic reticulum membrane;Golgi apparatus;Golgi lumen;integral component of plasma membrane;cell surface;membrane;integral component of membrane;Golgi-associated vesicle membrane;lysosomal lumen;glutamatergic synapse;GABA-ergic synapse;integral component of postsynaptic membrane
• Molecular function: protein binding;growth factor activity