CCN1

cellular communication network factor 1, the group of Cellular communication network factors

Basic information

Region (hg38): 1:85580761-85584589

Previous symbols: [ "IGFBP10", "CYR61" ]

Links

ENSG00000142871 ∙ NCBI:3491 ∙ OMIM:602369 ∙ HGNC:2654 ∙ Uniprot:O00622 ∙ 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 CCN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCN1 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
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	13	1	4

Variants in CCN1

This is a list of pathogenic ClinVar variants found in the CCN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-85580878-C-A			Benign (Nov 11, 2018)
1-85581000-G-T		not specified	Uncertain significance (Nov 15, 2021)
1-85581033-C-T		not specified	Uncertain significance (Apr 04, 2023)
1-85581241-G-A			Benign (Nov 11, 2018)
1-85581377-T-G		not specified	Uncertain significance (Nov 08, 2022)
1-85581408-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-85581431-G-T		not specified	Uncertain significance (Apr 20, 2024)
1-85581464-G-T		not specified	Uncertain significance (Sep 20, 2023)
1-85581628-G-C			Benign (Nov 12, 2018)
1-85582167-G-C		not specified	Uncertain significance (Feb 17, 2024)
1-85582439-C-G		not specified	Uncertain significance (Dec 16, 2022)
1-85582535-A-G		not specified	Uncertain significance (Jul 11, 2023)
1-85582538-A-G		not specified	Uncertain significance (Jul 30, 2023)
1-85582774-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-85582787-G-C		not specified	Uncertain significance (Apr 06, 2023)
1-85582796-C-T			Benign (May 03, 2018)
1-85582840-G-A		not specified	Uncertain significance (May 23, 2023)
1-85582842-T-G		not specified	Uncertain significance (Jan 10, 2023)
1-85582843-C-G			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCN1	protein_coding	protein_coding	ENST00000451137	5	3202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.714	0.286	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.366	201	216	0.930	0.0000119	2474
Missense in Polyphen		77	95.93	0.80267		1133
Synonymous	0.499	84	90.0	0.933	0.00000527	729
Loss of Function	3.18	3	17.2	0.174	8.99e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000951	0.0000924
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes cell proliferation, chemotaxis, angiogenesis and cell adhesion. Appears to play a role in wound healing by up- regulating, in skin fibroblasts, the expression of a number of genes involved in angiogenesis, inflammation and matrix remodeling including VEGA-A, VEGA-C, MMP1, MMP3, TIMP1, uPA, PAI-1 and integrins alpha-3 and alpha-5. CYR61-mediated gene regulation is dependent on heparin-binding. Down-regulates the expression of alpha-1 and alpha-2 subunits of collagen type-1. Promotes cell adhesion and adhesive signaling through integrin alpha-6/beta-1, cell migration through integrin alpha-v/beta-5 and cell proliferation through integrin alpha-v/beta-3. {ECO:0000269|PubMed:11584015}.

Recessive Scores

• pRec: 0.787

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.535
• hipred: Y
• hipred_score: 0.853
• ghis: 0.554

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccn1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; embryo phenotype; liver/biliary system phenotype; 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); 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)