CCN2

cellular communication network factor 2, the group of Cellular communication network factors

Basic information

Region (hg38): 6:131948176-131951372

Previous symbols: [ "CTGF" ]

Links

ENSG00000118523 ∙ NCBI:1490 ∙ OMIM:121009 ∙ HGNC:2500 ∙ Uniprot:P29279 ∙ 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 CCN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCN2 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
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	26	4	0

Variants in CCN2

This is a list of pathogenic ClinVar variants found in the CCN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-131949316-T-C		not specified	Uncertain significance (Mar 22, 2023)
6-131949382-T-C		not specified	Uncertain significance (Jan 24, 2023)
6-131949399-G-A			Likely benign (Oct 24, 2017)
6-131949410-G-C		not specified	Uncertain significance (Feb 26, 2024)
6-131949430-G-A		not specified	Uncertain significance (Feb 13, 2023)
6-131949493-G-T		not specified	Uncertain significance (Feb 11, 2022)
6-131949549-C-A		not specified	Uncertain significance (Jun 10, 2022)
6-131950005-G-T		not specified	Uncertain significance (Mar 23, 2023)
6-131950012-T-A			Likely benign (Jul 03, 2018)
6-131950057-C-T			Likely benign (Jul 18, 2018)
6-131950080-C-T		not specified	Uncertain significance (Sep 14, 2022)
6-131950313-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-131950319-G-C		not specified	Uncertain significance (Nov 10, 2022)
6-131950344-C-A		not specified	Uncertain significance (Nov 23, 2021)
6-131950418-T-C		not specified	Uncertain significance (Jan 19, 2024)
6-131950529-G-A			Likely benign (May 03, 2018)
6-131950549-G-A			Benign (Apr 01, 2024)
6-131950832-G-A		not specified	Uncertain significance (Aug 09, 2021)
6-131950847-C-T		not specified	Uncertain significance (Dec 05, 2022)
6-131950878-C-T		not specified	Uncertain significance (Jul 13, 2021)
6-131950903-G-C		not specified	Uncertain significance (Jun 18, 2021)
6-131950925-G-A		not specified	Uncertain significance (Sep 22, 2023)
6-131950935-G-C		not specified	Uncertain significance (Oct 25, 2023)
6-131950945-C-G		not specified	Uncertain significance (May 13, 2024)
6-131950947-C-G		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCN2	protein_coding	protein_coding	ENST00000367976	5	3198

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000502	0.890	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.521	163	183	0.892	0.00000936	2255
Missense in Polyphen		49	69.949	0.70051		795
Synonymous	0.979	65	75.8	0.857	0.00000436	663
Loss of Function	1.42	7	12.4	0.564	7.20e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major connective tissue mitoattractant secreted by vascular endothelial cells. Promotes proliferation and differentiation of chondrocytes. Mediates heparin- and divalent cation-dependent cell adhesion in many cell types including fibroblasts, myofibroblasts, endothelial and epithelial cells. Enhances fibroblast growth factor-induced DNA synthesis. {ECO:0000269|PubMed:10614647, ECO:0000269|PubMed:12553878}.

Recessive Scores

• pRec: 0.861

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.723
• hipred: Y
• hipred_score: 0.754
• ghis: 0.613

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccn2
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear phenotype; digestive/alimentary phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; embryo phenotype; skeleton phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: ccn2a
• Affected structure: myocardial precursor
• Phenotype tag: abnormal
• Phenotype quality: mislocalised laterally