CALML5

calmodulin like 5, the group of EF-hand domain containing

Basic information

Region (hg38): 10:5498697-5499570

Links

ENSG00000178372

∙ NCBI:51806 ∙ OMIM:605183 ∙ HGNC:18180 ∙ Uniprot:Q9NZT1 ∙ 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 CALML5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALML5 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			8 clinvar	2 clinvar		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in CALML5

This is a list of pathogenic ClinVar variants found in the CALML5 region.

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

Position	Phenotype	Significance	ClinVar
10-5499041-C-A	not specified	Uncertain significance (Feb 07, 2023)	2481473
10-5499042-G-A	not specified	Uncertain significance (May 24, 2023)	2569673
10-5499108-C-T	not specified	Uncertain significance (Sep 08, 2024)	3484429
10-5499122-G-C	not specified	Uncertain significance (Mar 11, 2024)	3136749
10-5499125-C-G	not specified	Uncertain significance (Jul 14, 2021)	2237038
10-5499141-C-G	not specified	Uncertain significance (Jan 10, 2022)	2385989
10-5499173-G-C	not specified	Uncertain significance (Mar 18, 2024)	3262992
10-5499198-C-G	not specified	Likely benign (Dec 10, 2024)	3484430
10-5499221-G-A	not specified	Likely benign (Apr 18, 2023)	2509298
10-5499263-T-G	not specified	Uncertain significance (Feb 28, 2025)	3826967
10-5499370-A-C	not specified	Uncertain significance (Sep 14, 2022)	2341675

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALML5	protein_coding	protein_coding	ENST00000380332	1	876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.720	85	106	0.803	0.00000793	938
Missense in Polyphen		23	31.408	0.7323		364
Synonymous	0.0405	54	54.4	0.993	0.00000512	288
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds calcium. May be involved in terminal differentiation of keratinocytes.;
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);Alzheimers Disease;Ras Signaling;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.0872

Intolerance Scores

loftool: 0.416
rvis_EVS: 0.64
rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

pHI: 0.0612
hipred: N
hipred_score: 0.317
ghis: 0.403

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.381

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Calm4
Phenotype

Gene ontology

Biological process: signal transduction;epidermis development;calcium-mediated signaling;neutrophil degranulation;regulation of catalytic activity
Cellular component: extracellular region;ficolin-1-rich granule lumen
Molecular function: calcium ion binding