CAPN9

calpain 9, the group of Calpains|EF-hand domain containing

Basic information

Region (hg38): 1:230747383-230802003

Links

ENSG00000135773 ∙ NCBI:10753 ∙ OMIM:606401 ∙ HGNC:1486 ∙ Uniprot:O14815 ∙ 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 CAPN9 gene.

• Inborn genetic diseases (40 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN9 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
missense			39	2		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	40	4	0

Variants in CAPN9

This is a list of pathogenic ClinVar variants found in the CAPN9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-230747509-T-C		not specified	Likely benign (Sep 12, 2023)
1-230747512-C-T		not specified	Uncertain significance (Dec 03, 2021)
1-230747513-G-A		not specified	Uncertain significance (Jun 30, 2023)
1-230747513-G-T		not specified	Uncertain significance (Jun 28, 2022)
1-230747592-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-230747665-T-G		not specified	Uncertain significance (Mar 27, 2023)
1-230747699-A-C		not specified	Uncertain significance (May 04, 2022)
1-230755343-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-230755383-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-230755390-C-G		not specified	Uncertain significance (Apr 13, 2023)
1-230755401-A-T		not specified	Uncertain significance (Feb 06, 2024)
1-230759516-C-G		not specified	Uncertain significance (Dec 01, 2022)
1-230759517-T-G		not specified	Uncertain significance (Apr 07, 2023)
1-230759531-C-T			Likely benign (Apr 01, 2022)
1-230759544-C-T		not specified	Uncertain significance (Jan 30, 2024)
1-230759548-C-T		not specified	Uncertain significance (Aug 17, 2021)
1-230759550-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-230759571-A-G		not specified	Uncertain significance (Dec 27, 2022)
1-230759604-G-A		not specified	Uncertain significance (Mar 31, 2023)
1-230759616-A-T		not specified	Uncertain significance (Dec 15, 2023)
1-230759618-A-T			Likely benign (Sep 01, 2022)
1-230762689-G-A		not specified	Uncertain significance (Aug 10, 2023)
1-230762743-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-230767656-G-A		not specified	Uncertain significance (Jul 31, 2023)
1-230767683-G-T		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN9	protein_coding	protein_coding	ENST00000271971	20	54620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-22	0.00867	122465	99	3184	125748	0.0131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0997	408	402	1.01	0.0000238	4580
Missense in Polyphen		169	165.9	1.0187		1856
Synonymous	0.678	151	162	0.932	0.0000104	1275
Loss of Function	0.808	37	42.7	0.867	0.00000227	458

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0145	0.0142
Ashkenazi Jewish	0.000697	0.000695
East Asian	0.0831	0.0820
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00375	0.00372
Middle Eastern	0.0831	0.0820
South Asian	0.0333	0.0329
Other	0.0105	0.0105

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease.
• Pathway: Integrin-mediated Cell Adhesion;Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.0901

Intolerance Scores

• loftool: 0.126
• rvis_EVS: 1.12
• rvis_percentile_EVS: 92.1

Haploinsufficiency Scores

• pHI: 0.0631
• hipred: N
• hipred_score: 0.289

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn9
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: proteolysis;digestion
• Cellular component: cellular_component;cytoplasm
• Molecular function: calcium-dependent cysteine-type endopeptidase activity;calcium ion binding