CCN5

cellular communication network factor 5, the group of Cellular communication network factors

Basic information

Region (hg38): 20:44714844-44728509

Previous symbols: [ "WISP2" ]

Links

ENSG00000064205 ∙ NCBI:8839 ∙ OMIM:603399 ∙ HGNC:12770 ∙ Uniprot:O76076 ∙ 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 CCN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCN5 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	2	3
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	2

Variants in CCN5

This is a list of pathogenic ClinVar variants found in the CCN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44715422-C-A		not specified	Uncertain significance (May 09, 2024)
20-44719916-C-T		not specified	Uncertain significance (Jan 08, 2024)
20-44719931-G-C		not specified	Uncertain significance (Jul 07, 2022)
20-44719939-C-G		not specified	Uncertain significance (Oct 26, 2022)
20-44719949-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-44719955-C-T		not specified	Uncertain significance (Dec 16, 2023)
20-44720072-A-T		not specified	Uncertain significance (Jan 10, 2023)
20-44720088-C-T		not specified	Likely benign (Jan 30, 2024)
20-44720096-G-A		not specified	Uncertain significance (Mar 01, 2023)
20-44720109-C-T			Benign (Feb 25, 2018)
20-44724789-G-T		not specified	Uncertain significance (Apr 04, 2024)
20-44724836-G-C		not specified	Uncertain significance (Sep 26, 2023)
20-44724864-G-T		not specified	Uncertain significance (Sep 30, 2022)
20-44724939-A-T		not specified	Uncertain significance (Nov 18, 2022)
20-44724965-C-T			Benign (Feb 25, 2018)
20-44724974-C-A		not specified	Uncertain significance (Jan 26, 2023)
20-44727131-C-A		not specified	Uncertain significance (Dec 30, 2023)
20-44727150-C-T		not specified	Uncertain significance (Mar 14, 2023)
20-44727197-C-T		not specified	Uncertain significance (Apr 07, 2022)
20-44727201-T-C		not specified	Uncertain significance (Nov 29, 2021)
20-44727252-T-C		not specified	Uncertain significance (May 13, 2024)
20-44727269-C-T		not specified	Uncertain significance (Jan 31, 2023)
20-44727281-C-T		not specified	Uncertain significance (Apr 07, 2022)
20-44727282-G-A		not specified	Uncertain significance (Mar 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCN5	protein_coding	protein_coding	ENST00000372868	4	13666

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000197	0.482	125709	0	35	125744	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.363	144	157	0.918	0.0000106	1546
Missense in Polyphen		47	56.977	0.82489		595
Synonymous	0.361	63	66.8	0.944	0.00000440	541
Loss of Function	0.534	8	9.80	0.816	5.04e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000974	0.0000924
European (Non-Finnish)	0.000179	0.000167
Middle Eastern	0.000110	0.000109
South Asian	0.0000658	0.0000653
Other	0.000844	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in modulating bone turnover. Promotes the adhesion of osteoblast cells and inhibits the binding of fibrinogen to integrin receptors. In addition, inhibits osteocalcin production.

Recessive Scores

• pRec: 0.163

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.360
• hipred: N
• hipred_score: 0.207
• ghis: 0.477

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Ccn5