CNN1

calponin 1

Basic information

Region (hg38): 19:11538767-11550323

Links

ENSG00000130176 ∙ NCBI:1264 ∙ OMIM:600806 ∙ HGNC:2155 ∙ Uniprot:P51911 ∙ 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 CNN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNN1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in CNN1

This is a list of pathogenic ClinVar variants found in the CNN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11538942-C-G		not specified	Uncertain significance (Dec 16, 2023)
19-11538976-G-A		not specified	Uncertain significance (Mar 31, 2024)
19-11541100-C-T		not specified	Uncertain significance (Sep 17, 2021)
19-11541101-G-A		not specified	Uncertain significance (Feb 23, 2023)
19-11541169-G-T		not specified	Uncertain significance (Sep 21, 2023)
19-11546889-G-A		not specified	Uncertain significance (Apr 07, 2022)
19-11546890-A-T		not specified	Uncertain significance (May 09, 2022)
19-11546892-A-G		not specified	Uncertain significance (May 25, 2022)
19-11547816-A-T		not specified	Uncertain significance (Dec 22, 2023)
19-11547867-C-A		not specified	Uncertain significance (Oct 22, 2021)
19-11549330-C-A		not specified	Uncertain significance (Dec 07, 2023)
19-11549337-G-C		not specified	Uncertain significance (Mar 07, 2023)
19-11549360-C-T		not specified	Uncertain significance (Jan 23, 2023)
19-11549374-C-T		not specified	Uncertain significance (Jan 18, 2023)
19-11549375-G-A		not specified	Uncertain significance (Apr 08, 2022)
19-11549377-C-T		not specified	Uncertain significance (Mar 23, 2022)
19-11549385-C-T			Likely benign (Sep 01, 2022)
19-11549626-A-G		not specified	Uncertain significance (Sep 17, 2021)
19-11549628-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-11549635-T-A		not specified	Uncertain significance (Aug 03, 2022)
19-11549671-G-A		not specified	Uncertain significance (Jan 10, 2022)
19-11549704-A-G		not specified	Uncertain significance (Oct 06, 2022)
19-11549766-C-G		not specified	Uncertain significance (Jun 05, 2023)
19-11549781-T-C		not specified	Uncertain significance (Dec 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNN1	protein_coding	protein_coding	ENST00000252456	7	11607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.138	0.858	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	143	190	0.752	0.0000120	1956
Missense in Polyphen		36	58.307	0.61742		660
Synonymous	-0.566	87	80.5	1.08	0.00000575	561
Loss of Function	2.52	4	14.3	0.280	6.12e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000334	0.0000334
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.000132	0.000131
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 (By similarity). {ECO:0000250}.
• Pathway: Endothelin Pathways;Myometrial Relaxation and Contraction Pathways (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.316
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.809
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnn1
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype; 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); cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of smooth muscle contraction;actomyosin structure organization;negative regulation of vascular smooth muscle cell proliferation
• Cellular component: cytoskeleton;focal adhesion
• Molecular function: actin binding;protein binding;calmodulin binding