GeneBe

CALML6

calmodulin like 6, the group of EF-hand domain containing

Basic information

Region (hg38): 1:1915108-1917296

Links

ENSG00000169885 ∙ NCBI:163688 ∙ OMIM:610171 ∙ HGNC:24193 ∙ Uniprot:Q8TD86 ∙ 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 CALML6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALML6 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
2
clinvar
 2
missense
6
clinvar
1
clinvar
 7
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 0 3

Variants in CALML6

This is a list of pathogenic ClinVar variants found in the CALML6 region.

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

Position Type Phenotype Significance ClinVar
1-1916468-A-G not specified Uncertain significance (Dec 17, 2023)3136750
1-1916483-G-A not specified Uncertain significance (Nov 29, 2023)2375736
1-1916569-C-T Benign (Apr 24, 2018)781580
1-1916599-G-T not specified Uncertain significance (Dec 19, 2022)2219327
1-1916758-G-C Benign (Apr 26, 2018)783273
1-1916758-G-T not specified Uncertain significance (Apr 14, 2022)3136751
1-1916786-A-G Benign (Apr 26, 2018)719694
1-1916793-G-A not specified Uncertain significance (Jun 02, 2024)3262993
1-1916829-G-C not specified Uncertain significance (Feb 12, 2024)3136752
1-1917005-A-G not specified Uncertain significance (Jan 05, 2022)2320755

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CALML6protein_codingprotein_codingENST00000307786 62470
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.61e-80.08761256310251256560.0000995
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.05151021030.9860.000005731204
Missense in Polyphen3028.2391.0624352
Synonymous-0.02764342.81.010.00000312302
Loss of Function-0.332119.881.114.19e-7118

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001530.000152
Ashkenazi Jewish0.00009940.0000993
East Asian0.00005440.0000544
Finnish0.00009240.0000924
European (Non-Finnish)0.0001100.000106
Middle Eastern0.00005440.0000544
South Asian0.0001330.000131
Other0.0003360.000326

dbNSFP

Source: dbNSFP

Pathway
Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Pertussis - Homo sapiens (human);Long-term potentiation - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Circadian entrainment - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Glioma - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Renin secretion - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Olfactory transduction - Homo sapiens (human);Phototransduction - Homo sapiens (human);Alcoholism - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Ras Signaling (Consensus)

Recessive Scores

pRec
0.150

Intolerance Scores

loftool
0.538
rvis_EVS
0.13
rvis_percentile_EVS
63.2

Haploinsufficiency Scores

pHI
0.121
hipred
N
hipred_score
0.341
ghis
0.406

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.333

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
calcium-mediated signaling;regulation of catalytic activity
Cellular component
cytoplasm
Molecular function
calcium ion binding