CAMK1

calcium/calmodulin dependent protein kinase I, the group of Calmodulin dependent protein kinases

Basic information

Region (hg38): 3:9757346-9769992

Links

ENSG00000134072 ∙ NCBI:8536 ∙ OMIM:604998 ∙ HGNC:1459 ∙ Uniprot:Q14012 ∙ 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 CAMK1 gene.

• Inborn genetic diseases (14 variants)
• not provided (2 variants)
• Nonpapillary renal cell carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMK1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	15	2	0

Variants in CAMK1

This is a list of pathogenic ClinVar variants found in the CAMK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-9757579-G-A		not specified	Uncertain significance (Oct 12, 2021)
3-9757618-G-A		not specified	Uncertain significance (Dec 13, 2022)
3-9757767-G-A		not specified	Uncertain significance (Nov 12, 2021)
3-9757813-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-9759573-A-G		not specified	Uncertain significance (Aug 23, 2021)
3-9759702-A-G		not specified	Uncertain significance (Dec 05, 2022)
3-9760718-T-G		not specified	Uncertain significance (Feb 15, 2023)
3-9761529-T-G		not specified	Uncertain significance (Jul 16, 2021)
3-9761736-T-C		not specified	Uncertain significance (Aug 22, 2023)
3-9762926-G-C		not specified	Uncertain significance (Sep 12, 2023)
3-9762987-C-G		not specified	Uncertain significance (Aug 31, 2022)
3-9763155-A-G		not specified	Uncertain significance (Oct 17, 2023)
3-9763173-C-T		not specified	Uncertain significance (Aug 22, 2023)
3-9763184-T-C		not specified	Uncertain significance (Aug 12, 2022)
3-9763195-A-G			Likely benign (Jan 01, 2023)
3-9765858-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-9765879-G-A			Uncertain significance (Jul 01, 2022)
3-9765903-G-A		Nonpapillary renal cell carcinoma	Likely benign (May 10, 2017)
3-9765935-C-T		OGG1-related disorder	Likely benign (Jul 12, 2019)
3-9766058-G-A		not specified	Uncertain significance (Sep 01, 2021)
3-9767725-T-C		not specified	Uncertain significance (Sep 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMK1	protein_coding	protein_coding	ENST00000256460	11	12651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000301	0.987	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	201	223	0.901	0.0000129	2444
Missense in Polyphen		82	101.05	0.81147		1158
Synonymous	-0.0763	95	94.1	1.01	0.00000630	690
Loss of Function	2.21	11	22.3	0.494	0.00000114	243

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000272	0.000272
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium/calmodulin-dependent protein kinase that operates in the calcium-triggered CaMKK-CaMK1 signaling cascade and, upon calcium influx, regulates transcription activators activity, cell cycle, hormone production, cell differentiation, actin filament organization and neurite outgrowth. Recognizes the substrate consensus sequence [MVLIF]-x-R-x(2)-[ST]-x(3)-[MVLIF]. Regulates axonal extension and growth cone motility in hippocampal and cerebellar nerve cells. Upon NMDA receptor-mediated Ca(2+) elevation, promotes dendritic growth in hippocampal neurons and is essential in synapses for full long-term potentiation (LTP) and ERK2-dependent translational activation. Downstream of NMDA receptors, promotes the formation of spines and synapses in hippocampal neurons by phosphorylating ARHGEF7/BETAPIX on 'Ser- 694', which results in the enhancement of ARHGEF7 activity and activation of RAC1. Promotes neuronal differentiation and neurite outgrowth by activation and phosphorylation of MARK2 on 'Ser-91', 'Ser-92', 'Ser-93' and 'Ser-294'. Promotes nuclear export of HDAC5 and binding to 14-3-3 by phosphorylation of 'Ser-259' and 'Ser- 498' in the regulation of muscle cell differentiation. Regulates NUMB-mediated endocytosis by phosphorylation of NUMB on 'Ser-276' and 'Ser-295'. Involved in the regulation of basal and estrogen- stimulated migration of medulloblastoma cells through ARHGEF7/BETAPIX phosphorylation (By similarity). Is required for proper activation of cyclin-D1/CDK4 complex during G1 progression in diploid fibroblasts. Plays a role in K(+) and ANG2-mediated regulation of the aldosterone synthase (CYP11B2) to produce aldosterone in the adrenal cortex. Phosphorylates EIF4G3/eIF4GII. In vitro phosphorylates CREB1, ATF1, CFTR, MYL9 and SYN1/synapsin I. {ECO:0000250, ECO:0000269|PubMed:11114197, ECO:0000269|PubMed:12193581, ECO:0000269|PubMed:14507913, ECO:0000269|PubMed:14754892, ECO:0000269|PubMed:17056143, ECO:0000269|PubMed:17442826, ECO:0000269|PubMed:18184567, ECO:0000269|PubMed:20181577}.
• Pathway: Aldosterone synthesis and secretion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Association Between Physico-Chemical Features and Toxicity Associated Pathways;Pathways in clear cell renal cell carcinoma;Calcium Regulation in the Cardiac Cell (Consensus)

Recessive Scores

• pRec: 0.187

Intolerance Scores

• loftool: 0.720
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.244
• hipred: Y
• hipred_score: 0.718
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Camk1
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein phosphorylation;nucleocytoplasmic transport;cell cycle;signal transduction;positive regulation of neuron projection development;negative regulation of protein binding;regulation of protein localization;positive regulation of peptidyl-serine phosphorylation;regulation of protein binding;positive regulation of transcription by RNA polymerase II;positive regulation of protein export from nucleus;regulation of muscle cell differentiation;positive regulation of muscle cell differentiation;positive regulation of synapse structural plasticity;positive regulation of syncytium formation by plasma membrane fusion;positive regulation of dendritic spine development;positive regulation of protein serine/threonine kinase activity;positive regulation of protein acetylation;regulation of histone H3-K9 acetylation
• Cellular component: nucleus;cytoplasm;postsynaptic density;glutamatergic synapse
• Molecular function: calmodulin-dependent protein kinase activity;protein binding;calmodulin binding;ATP binding