CAMK2N1

calcium/calmodulin dependent protein kinase II inhibitor 1

Basic information

Region (hg38): 1:20482391-20486210

Links

ENSG00000162545

∙ NCBI:55450 ∙ OMIM:614986 ∙ HGNC:24190 ∙ Uniprot:Q7Z7J9 ∙ 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 CAMK2N1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMK2N1 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in CAMK2N1

This is a list of pathogenic ClinVar variants found in the CAMK2N1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20485358-C-G		not specified	Uncertain significance (Sep 29, 2023)	3136796

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMK2N1	protein_coding	protein_coding	ENST00000375078	2	3830

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.167	0.654	124777	0	1	124778	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	14	39.5	0.354	0.00000191	501
Missense in Polyphen		3	8.7525	0.34276		100
Synonymous	1.05	12	17.6	0.682	9.34e-7	146
Loss of Function	0.798	1	2.31	0.433	9.90e-8	29

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Potent and specific inhibitor of CaM-kinase II (CAMK2). {ECO:0000250, ECO:0000269|PubMed:18305109}.;

Intolerance Scores

loftool: 0.333
rvis_EVS: 0.1
rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

pHI: 0.324
hipred: N
hipred_score: 0.421
ghis: 0.564

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.231

Mouse Genome Informatics

Gene name: Camk2n1
Phenotype

Zebrafish Information Network

Gene name: camk2n1a
Affected structure: ventricular system
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: negative regulation of protein kinase activity;negative regulation of cell population proliferation;positive regulation of gene expression;negative regulation of cell cycle;negative regulation of proteolysis;negative regulation of ERK1 and ERK2 cascade;negative regulation of cyclin-dependent protein kinase activity
Cellular component: cellular_component;postsynaptic density;cell junction;dendrite;neuronal cell body;postsynaptic membrane
Molecular function: calcium-dependent protein kinase inhibitor activity;protein kinase binding