CAMK1D

calcium/calmodulin dependent protein kinase ID, the group of MicroRNA protein coding host genes|Calmodulin dependent protein kinases

Basic information

Region (hg38): 10:12349547-12835545

Links

ENSG00000183049 ∙ NCBI:57118 ∙ OMIM:607957 ∙ HGNC:19341 ∙ Uniprot:Q8IU85 ∙ 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 CAMK1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAMK1D 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	2
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	9	1	2

Variants in CAMK1D

This is a list of pathogenic ClinVar variants found in the CAMK1D region.

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

Position	Type	Phenotype	Significance	ClinVar
10-12553253-G-A		not specified	Uncertain significance (Aug 20, 2023)
10-12553305-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-12553330-A-G			Benign (Feb 07, 2018)
10-12553340-A-G		not specified	Uncertain significance (Dec 20, 2023)
10-12666785-A-C		not specified	Uncertain significance (Mar 31, 2023)
10-12760948-G-C		not specified	Likely benign (Oct 20, 2023)
10-12760972-C-T			Benign (Jun 01, 2018)
10-12791169-C-G		not specified	Uncertain significance (Jan 02, 2024)
10-12816301-C-T		not specified	Uncertain significance (Jan 03, 2024)
10-12816319-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-12824507-C-T			Likely benign (Feb 07, 2018)
10-12828796-T-C		not specified	Uncertain significance (Jan 24, 2023)
10-12828834-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAMK1D	protein_coding	protein_coding	ENST00000378847	11	486065

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00380	125653	0	93	125746	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.49	124	230	0.539	0.0000134	2547
Missense in Polyphen		14	69.758	0.20069		814
Synonymous	-0.261	98	94.8	1.03	0.00000642	698
Loss of Function	4.03	1	20.9	0.0480	8.82e-7	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000862	0.000854
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000652	0.000647
European (Non-Finnish)	0.000459	0.000457
Middle Eastern	0.000273	0.000272
South Asian	0.00	0.00
Other	0.000984	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium/calmodulin-dependent protein kinase that operates in the calcium-triggered CaMKK-CaMK1 signaling cascade and, upon calcium influx, activates CREB-dependent gene transcription, regulates calcium-mediated granulocyte function and respiratory burst and promotes basal dendritic growth of hippocampal neurons. In neutrophil cells, required for cytokine- induced proliferative responses and activation of the respiratory burst. Activates the transcription factor CREB1 in hippocampal neuron nuclei. May play a role in apoptosis of erythroleukemia cells. In vitro, phosphorylates transcription factor CREM isoform Beta. {ECO:0000269|PubMed:11050006, ECO:0000269|PubMed:15840691, ECO:0000269|PubMed:16324104, ECO:0000269|PubMed:17056143}.
• Pathway: Aldosterone synthesis and secretion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.0786
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.765
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.767

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Camk1d

Zebrafish Information Network

• Gene name: camk1da
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: protein phosphorylation;inflammatory response;positive regulation of neuron projection development;positive regulation of CREB transcription factor activity;positive regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of phagocytosis;regulation of dendrite development;positive regulation of respiratory burst;regulation of granulocyte chemotaxis;positive regulation of neutrophil chemotaxis
• Cellular component: nucleus;cytoplasm
• Molecular function: calmodulin-dependent protein kinase activity;calmodulin binding;ATP binding