CALML4

calmodulin like 4, the group of EF-hand domain containing

Basic information

Region (hg38): 15:68190705-68206079

Links

ENSG00000129007 ∙ NCBI:91860 ∙ ∙ HGNC:18445 ∙ Uniprot:Q96GE6 ∙ 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 CALML4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALML4 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			12	3		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	14	3	0

Variants in CALML4

This is a list of pathogenic ClinVar variants found in the CALML4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-68194022-TC-T			not provided (-)
15-68194077-T-C		not specified	Uncertain significance (Jun 25, 2024)
15-68194086-T-A		not specified	Uncertain significance (Jan 17, 2025)
15-68194086-T-G		not specified	Uncertain significance (Nov 17, 2023)
15-68194088-T-C		not specified	Likely benign (Oct 21, 2021)
15-68197485-G-A		not specified	Uncertain significance (Sep 20, 2024)
15-68197489-G-T		not specified	Likely benign (Oct 25, 2024)
15-68197503-C-T		not specified	Likely benign (Jul 14, 2023)
15-68197524-C-T		not specified	Uncertain significance (May 28, 2024)
15-68197535-A-G		not specified	Uncertain significance (Apr 09, 2024)
15-68197542-G-C		not specified	Uncertain significance (Nov 30, 2021)
15-68197545-G-C		not specified	Uncertain significance (Mar 03, 2025)
15-68197569-G-C		not specified	Uncertain significance (Apr 04, 2023)
15-68197601-G-A		not specified	Uncertain significance (Jun 16, 2024)
15-68199547-C-T		not specified	Uncertain significance (Jul 14, 2024)
15-68199552-G-C		not specified	Uncertain significance (Sep 14, 2022)
15-68199567-T-C		not specified	Uncertain significance (Jan 04, 2025)
15-68199597-A-C		not specified	Uncertain significance (Jan 27, 2025)
15-68205133-C-A		not specified	Uncertain significance (Sep 10, 2024)
15-68205270-G-C		not specified	Uncertain significance (Mar 20, 2023)
15-68205316-C-T		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALML4	protein_coding	protein_coding	ENST00000467889	5	15375

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000592	0.480	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.701	141	119	1.18	0.00000671	1294
Missense in Polyphen		41	39.728	1.032		505
Synonymous	0.578	42	47.0	0.893	0.00000285	369
Loss of Function	0.434	7	8.35	0.838	3.51e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000610	0.000606
Ashkenazi Jewish	0.00	0.00
East Asian	0.000333	0.000326
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000333	0.000326
South Asian	0.000327	0.000327
Other	0.000166	0.000163

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: 0.0896

Intolerance Scores

• loftool: 0.647
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.171
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calml4

Gene ontology

• Biological process: calcium-mediated signaling;regulation of catalytic activity
• Molecular function: calcium ion binding