CCN4

cellular communication network factor 4, the group of Cellular communication network factors

Basic information

Region (hg38): 8:133191038-133231690

Previous symbols: [ "WISP1-OT1", "WISP1-UT1", "WISP1" ]

Links

ENSG00000104415 ∙ NCBI:8840 ∙ OMIM:603398 ∙ HGNC:12769 ∙ Uniprot:O95388 ∙ 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 CCN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCN4 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			32	1	1	34
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	32	4	3

Variants in CCN4

This is a list of pathogenic ClinVar variants found in the CCN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-133191172-G-A		not specified	Uncertain significance (Jan 20, 2023)
8-133191173-C-A		not specified	Uncertain significance (Jan 20, 2023)
8-133191178-G-A		not specified	Uncertain significance (Jan 20, 2023)
8-133191182-C-T		not specified	Uncertain significance (Feb 27, 2024)
8-133191202-G-A		not specified	Uncertain significance (Jun 23, 2021)
8-133212982-C-T		not specified	Uncertain significance (Oct 06, 2023)
8-133213085-G-A			Benign (Apr 10, 2018)
8-133213091-C-T			Benign (Feb 26, 2018)
8-133213117-C-T		not specified	Uncertain significance (Mar 31, 2024)
8-133213129-T-G		not specified	Uncertain significance (Nov 07, 2022)
8-133220601-G-A		not specified	Uncertain significance (Aug 02, 2023)
8-133220632-A-G		not specified	Uncertain significance (Jun 16, 2024)
8-133220665-C-T			Likely benign (Aug 29, 2018)
8-133220675-C-T			Likely benign (Apr 12, 2018)
8-133220676-G-A		not specified	Uncertain significance (Aug 10, 2021)
8-133220707-G-A		not specified	Uncertain significance (May 06, 2024)
8-133220712-C-T		not specified	Uncertain significance (Jan 19, 2022)
8-133220719-C-T		not specified	Uncertain significance (Sep 26, 2022)
8-133220721-C-T		not specified	Uncertain significance (May 05, 2023)
8-133220722-G-A		not specified	Uncertain significance (Sep 26, 2022)
8-133220740-C-T		not specified	Uncertain significance (Nov 22, 2021)
8-133220743-G-A		not specified	Uncertain significance (Jan 18, 2023)
8-133220746-G-A		not specified	Uncertain significance (Sep 16, 2021)
8-133220755-T-A		not specified	Uncertain significance (Dec 15, 2022)
8-133220769-T-G		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCN4	protein_coding	protein_coding	ENST00000250160	5	39306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.39e-7	0.702	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	236	246	0.961	0.0000159	2397
Missense in Polyphen		81	100.31	0.8075		1023
Synonymous	-1.11	111	97.0	1.14	0.00000667	723
Loss of Function	1.18	12	17.3	0.695	0.00000102	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000330
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000274	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000974	0.0000967
Middle Eastern	0.000274	0.000272
South Asian	0.000231	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Downstream regulator in the Wnt/Frizzled-signaling pathway. Associated with cell survival. Attenuates p53-mediated apoptosis in response to DNA damage through activation of AKT kinase. Up-regulates the anti-apoptotic Bcl-X(L) protein. Adheres to skin and melanoma fibroblasts. In vitro binding to skin fibroblasts occurs through the proteoglycans, decorin and biglycan. {ECO:0000269|PubMed:10716946, ECO:0000269|PubMed:11782444}.

Recessive Scores

• pRec: 0.164

Intolerance Scores

• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.18

Haploinsufficiency Scores

• pHI: 0.365
• hipred: N
• hipred_score: 0.250
• ghis: 0.447

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccn4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)