CALU

calumenin, the group of CREC family

Basic information

Region (hg38): 7:128739291-128773400

Links

ENSG00000128595 ∙ NCBI:813 ∙ OMIM:603420 ∙ HGNC:1458 ∙ Uniprot:O43852 ∙ 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 CALU gene.

• not provided (25 variants)
• Inborn genetic diseases (13 variants)
• Developmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CALU 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			9			9
nonsense		1	1			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			16	10	1	27
Total	0	1	26	10	1

Variants in CALU

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

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

Position	Type	Phenotype	Significance	ClinVar
7-128748365-C-G		not specified	Uncertain significance (Feb 28, 2023)
7-128748663-G-A		not specified	Uncertain significance (Nov 03, 2023)
7-128754267-T-C		not specified	Uncertain significance (Nov 17, 2022)
7-128754302-G-C		not specified	Uncertain significance (Jun 29, 2023)
7-128754308-G-A		not specified	Uncertain significance (Dec 20, 2021)
7-128754404-G-A		not specified	Uncertain significance (Oct 27, 2022)
7-128758947-C-G		not specified	Uncertain significance (Aug 04, 2021)
7-128759009-A-G		not specified	Uncertain significance (Dec 08, 2023)
7-128767473-G-C		not specified	Uncertain significance (Nov 09, 2021)
7-128767512-C-T		Developmental disorder	Likely pathogenic (Nov 10, 2022)
7-128767546-G-A		not specified	Uncertain significance (Jul 14, 2023)
7-128769067-G-A		not specified	Uncertain significance (Jul 09, 2021)
7-128769151-G-A		not specified	Uncertain significance (Feb 27, 2023)
7-128772544-T-C			Uncertain significance (Mar 10, 2022)
7-128772550-C-T			Uncertain significance (Mar 20, 2022)
7-128772564-C-A		OPN1SW-related disorder	Benign/Likely benign (Jan 29, 2024)
7-128772564-C-T			Likely benign (Sep 01, 2023)
7-128772566-A-G		not specified	Uncertain significance (Aug 02, 2021)
7-128772567-G-A			Likely benign (Jan 25, 2024)
7-128772570-A-C			Likely benign (Mar 25, 2020)
7-128772571-G-A			Uncertain significance (Feb 24, 2022)
7-128772574-G-A			Uncertain significance (Aug 31, 2022)
7-128772582-T-G			Likely benign (Jul 19, 2022)
7-128772592-G-T			Uncertain significance (Feb 01, 2022)
7-128772600-T-C			Likely benign (May 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CALU	protein_coding	protein_coding	ENST00000542996	7	32516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0140	0.980	125543	0	7	125550	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	128	177	0.724	0.00000896	2211
Missense in Polyphen		48	75.917	0.63227		966
Synonymous	0.0400	60	60.4	0.993	0.00000305	514
Loss of Function	2.42	6	16.6	0.360	8.72e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in regulation of vitamin K-dependent carboxylation of multiple N-terminal glutamate residues. Seems to inhibit gamma-carboxylase GGCX. Binds 7 calcium ions with a low affinity (By similarity). {ECO:0000250}.
• Pathway: Warfarin Pathway, Pharmacodynamics;NOTCH1 regulation of human endothelial cell calcification;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.420

Intolerance Scores

• loftool: 0.422
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.657
• hipred: Y
• hipred_score: 0.859
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Calu

Gene ontology

• Biological process: biological_process;post-translational protein modification;cellular protein metabolic process
• Cellular component: extracellular region;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;Golgi apparatus;membrane;sarcoplasmic reticulum lumen;melanosome
• Molecular function: calcium ion binding;protein binding