CAPN15

calpain 15, the group of MicroRNA protein coding host genes|Zinc fingers RANBP2-type |Calpains

Basic information

Region (hg38): 16:527712-554636

Previous symbols: [ "SOLH" ]

Links

ENSG00000103326 ∙ NCBI:6650 ∙ OMIM:603267 ∙ HGNC:11182 ∙ Uniprot:O75808 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oculogastrointestinal-neurodevelopmental syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oculogastrointestinal neurodevelopmental syndrome	AR	Cardiovascular	Individuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and management	Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal	32885237; 33410501

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPN15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN15 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				48	9	57
missense			109	11	1	121
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	2	6
non coding			1		1	2
Total	0	1	110	59	11

Variants in CAPN15

This is a list of pathogenic ClinVar variants found in the CAPN15 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-546851-G-A		not specified	Uncertain significance (Aug 30, 2022)
16-546888-C-T		not specified	Uncertain significance (Dec 15, 2022)
16-546893-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-546893-G-T		Oculogastrointestinal-neurodevelopmental syndrome	Uncertain significance (Feb 18, 2022)
16-546938-G-A		not specified	Uncertain significance (Jun 03, 2024)
16-546957-G-A		not specified	Uncertain significance (Sep 09, 2021)
16-546960-T-G		not specified	Uncertain significance (Jul 13, 2021)
16-546972-A-G		not specified	Uncertain significance (Oct 29, 2021)
16-546989-G-T		not specified	Uncertain significance (Mar 22, 2023)
16-546992-C-T		not specified	Uncertain significance (Dec 27, 2022)
16-546993-G-T		not specified	Uncertain significance (Aug 22, 2023)
16-547029-G-A		not specified	Uncertain significance (Apr 27, 2024)
16-547030-C-T		CAPN15-related disorder	Likely benign (Jun 13, 2019)
16-547059-C-T		CAPN15-related disorder	Likely benign (Sep 01, 2022)
16-547080-C-G		not specified	Uncertain significance (Jul 14, 2022)
16-547094-G-C		not specified	Uncertain significance (Aug 19, 2023)
16-547112-G-A		CAPN15-related disorder • not specified	Likely benign (Jun 10, 2022)
16-547150-A-G		CAPN15-related disorder	Benign (Sep 12, 2019)
16-547171-G-A			Likely benign (Aug 01, 2022)
16-547206-G-T		not specified	Uncertain significance (Dec 21, 2023)
16-547213-C-A		not specified	Likely benign (Jun 06, 2022)
16-547222-G-C		not specified	Uncertain significance (Sep 22, 2023)
16-547229-A-C		not specified	Likely benign (Jun 11, 2024)
16-547229-A-G			Likely benign (Jul 01, 2023)
16-547247-G-A		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN15	protein_coding	protein_coding	ENST00000219611	11	26920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0314	124318	10	974	125302	0.00393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	578	711	0.813	0.0000519	6848
Missense in Polyphen		214	348.22	0.61455		3242
Synonymous	-4.46	447	342	1.31	0.0000292	2314
Loss of Function	4.97	7	41.6	0.168	0.00000222	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00457	0.00452
Ashkenazi Jewish	0.00717	0.00599
East Asian	0.0000545	0.0000544
Finnish	0.00153	0.00139
European (Non-Finnish)	0.00694	0.00612
Middle Eastern	0.0000545	0.0000544
South Asian	0.00126	0.00114
Other	0.00643	0.00590

dbNSFP

Source: dbNSFP

• Pathway: Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.120

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.728
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn15

Gene ontology

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