CCN6

cellular communication network factor 6, the group of Cellular communication network factors

Basic information

Region (hg38): 6:112054075-112069686

Previous symbols: [ "WISP3" ]

Links

ENSG00000112761

∙ NCBI:8838 ∙ OMIM:603400 ∙ HGNC:12771 ∙ Uniprot:O95389 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

progressive pseudorheumatoid arthropathy of childhood (Supportive), mode of inheritance: AR
progressive pseudorheumatoid arthropathy of childhood (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Progressive pseudorheumatoid dysplasia	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	6807993; 6410512; 6873109; 6431106; 8275575; 9222963; 10471507; 16152649; 19064006; 21528827

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCN6 gene.

not_provided (190 variants)
Progressive_pseudorheumatoid_dysplasia (58 variants)
Inborn_genetic_diseases (36 variants)
CCN6-related_disorder (10 variants)
not_specified (8 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCN6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198239.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	51 clinvar	4 clinvar	56
missense	6 clinvar	8 clinvar	63 clinvar	9 clinvar	4 clinvar	90
nonsense	11 clinvar	3 clinvar				14
start loss	3	1				4
frameshift	27 clinvar	4 clinvar	1 clinvar			32
splice donor/acceptor (+/-2bp)	2 clinvar	2 clinvar				4
Total	49	18	65	60	8

Highest pathogenic variant AF is 0.000149348

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCN6	protein_coding	protein_coding	ENST00000361714	5	16897

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000619	0.979	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.161	184	190	0.967	0.00000920	2435
Missense in Polyphen		65	76.724	0.8472		983
Synonymous	0.324	64	67.4	0.950	0.00000335	691
Loss of Function	2.04	8	17.1	0.467	8.21e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000163	0.000163
South Asian	0.000261	0.000261
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Appears to be required for normal postnatal skeletal growth and cartilage homeostasis.;

Recessive Scores

pRec: 0.152

Intolerance Scores

loftool
rvis_EVS: 1.02
rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

pHI: 0.0860
hipred: N
hipred_score: 0.294
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name: Ccn6
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); neoplasm; normal phenotype;

Zebrafish Information Network

Gene name: ccn6
Affected structure: pharyngeal arch cartilage
Phenotype tag: abnormal
Phenotype quality: fragile