CNN2

calponin 2

Basic information

Region (hg38): 19:1026586-1039068

Links

ENSG00000064666 ∙ NCBI:1265 ∙ OMIM:602373 ∙ HGNC:2156 ∙ Uniprot:Q99439 ∙ 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 CNN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNN2 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						0
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in CNN2

This is a list of pathogenic ClinVar variants found in the CNN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1031110-C-T		not specified	Uncertain significance (May 24, 2024)
19-1032412-C-T		not specified	Uncertain significance (Feb 14, 2024)
19-1032448-A-G		not specified	Uncertain significance (May 26, 2023)
19-1032562-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-1032655-A-G		not specified	Uncertain significance (Sep 27, 2022)
19-1032682-G-T		not specified	Uncertain significance (Oct 12, 2021)
19-1032691-G-A		not specified	Uncertain significance (Dec 09, 2023)
19-1036169-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-1036202-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-1036205-G-A		not specified	Uncertain significance (Jun 04, 2024)
19-1036232-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-1037649-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-1037687-G-T		not specified	Uncertain significance (Mar 13, 2023)
19-1037725-C-T		not specified	Uncertain significance (Jun 07, 2023)
19-1037737-A-T		not specified	Uncertain significance (Feb 27, 2023)
19-1037757-G-A		Pulmonary artery atresia	Pathogenic (-)
19-1037767-G-A		Pulmonary artery atresia	Pathogenic (-)
19-1037811-G-A		not specified	Uncertain significance (Jul 16, 2021)
19-1037830-C-G		not specified	Uncertain significance (Jun 07, 2024)
19-1037862-G-C		not specified	Uncertain significance (Jan 17, 2023)
19-1037896-A-G		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNN2	protein_coding	protein_coding	ENST00000263097	7	12771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0244	0.963	125717	0	15	125732	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.152	210	204	1.03	0.0000130	2023
Missense in Polyphen		32	39.6	0.80808		512
Synonymous	-1.11	105	91.5	1.15	0.00000701	581
Loss of Function	2.19	5	13.8	0.363	6.86e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000874	0.0000874
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000528
Middle Eastern	0.000109	0.000109
South Asian	0.0000985	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C and tropomyosin. The interaction of calponin with actin inhibits the actomyosin Mg-ATPase activity.
• Pathway: Myometrial Relaxation and Contraction Pathways;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.224
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.156
• hipred: Y
• hipred_score: 0.530
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.411

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cnn2
• Phenotype: hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: cytoskeleton organization;actomyosin structure organization;regulation of actin filament-based process;interleukin-12-mediated signaling pathway;neutrophil degranulation;cellular response to mechanical stimulus
• Cellular component: stress fiber;extracellular region;cytoskeleton;cell-cell junction;focal adhesion;membrane;specific granule lumen;tertiary granule lumen
• Molecular function: actin binding;calmodulin binding;cadherin binding