CAPN12

calpain 12, the group of Calpains|EF-hand domain containing

Basic information

Region (hg38): 19:38730186-38769904

Links

ENSG00000182472 ∙ NCBI:147968 ∙ OMIM:608839 ∙ HGNC:13249 ∙ Uniprot:Q6ZSI9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Disputed Evidence), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAPN12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAPN12 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				18	9	27
missense			67	7	8	82
nonsense			2	1		3
start loss						0
frameshift				1		1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region			1	2	3	6
non coding				2	34	36
Total	0	0	69	30	51

Variants in CAPN12

This is a list of pathogenic ClinVar variants found in the CAPN12 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38730655-A-G			Benign (Jul 09, 2018)
19-38730845-G-A		CAPN12-related disorder	Likely benign (Jul 15, 2019)
19-38730884-G-A		CAPN12-related disorder	Benign (Oct 28, 2019)
19-38731001-A-C		not specified	Uncertain significance (Aug 02, 2021)
19-38731007-G-A		CAPN12-related disorder	Likely benign (Sep 17, 2019)
19-38731019-G-A		CAPN12-related disorder	Likely benign (Dec 01, 2023)
19-38731021-G-A		not specified	Uncertain significance (Mar 07, 2023)
19-38731075-CCCATGCCCCA-C			Benign (Jul 09, 2018)
19-38731123-G-A			Likely benign (Jul 01, 2022)
19-38731141-G-A		CAPN12-related disorder	Benign (Dec 31, 2019)
19-38731145-C-A			Uncertain significance (Dec 01, 2023)
19-38731145-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-38731146-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-38731149-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-38731161-G-A		not specified	Uncertain significance (May 20, 2024)
19-38731175-C-T		not specified	Uncertain significance (May 13, 2024)
19-38731181-C-T		not specified	Uncertain significance (May 31, 2023)
19-38731182-G-A		CAPN12-related disorder	Benign (Oct 28, 2019)
19-38731184-C-G		not specified	Uncertain significance (Apr 24, 2024)
19-38731207-G-C		not specified	Uncertain significance (Oct 06, 2021)
19-38731209-T-G		not specified	Uncertain significance (Jul 25, 2023)
19-38731307-A-T			Benign (Jul 09, 2018)
19-38733450-G-C			Benign (Jul 09, 2018)
19-38733696-T-TC		CAPN12-related disorder	Benign (Feb 22, 2019)
19-38733723-C-T		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAPN12	protein_coding	protein_coding	ENST00000328867	21	39718

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-33	9.99e-7	125180	2	566	125748	0.00226

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.26	510	436	1.17	0.0000279	4611
Missense in Polyphen		205	178.6	1.1478		1822
Synonymous	-3.03	238	186	1.28	0.0000121	1453
Loss of Function	-1.09	46	38.7	1.19	0.00000166	436

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00706	0.00692
Ashkenazi Jewish	0.000714	0.000695
East Asian	0.00210	0.00207
Finnish	0.000978	0.000971
European (Non-Finnish)	0.00140	0.00138
Middle Eastern	0.00210	0.00207
South Asian	0.00590	0.00586
Other	0.00215	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-regulated non-lysosomal thiol-protease. {ECO:0000250}.
• Pathway: Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.334
• rvis_EVS: -0.52
• rvis_percentile_EVS: 20.94

Haploinsufficiency Scores

• pHI: 0.390
• hipred: N
• hipred_score: 0.170
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Capn12

Zebrafish Information Network

• Gene name: capn12
• Affected structure: keratinocyte
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

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