CALR3 (calreticulin 3)

Gene

• Entrez ID: 125972
• Gene name: Calreticulin 3
• Gene symbol: CALR3
• Synonyms (NCBI Gene): CMH19, CRT2, CT93
• Chromosome: 19
• Chromosome location: 19p13.11
• Summary: The protein encoded by this gene belongs to the calreticulin family, members of which are calcium-binding chaperones localized mainly in the endoplasmic reticulum. This protein is also localized to the endoplasmic reticulum lumen, however, its capacity fo

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs142951029	T>C,G	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs182376945	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs747656642	A>-	Conflicting-interpretations-of-pathogenicity	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT859774	hsa-miR-4450	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005509	Function	Calcium ion binding	IDA	21590275
GO:0005635	Component	Nuclear envelope	IDA	21590275
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005788	Component	Endoplasmic reticulum lumen	IDA	21590275
GO:0005788	Component	Endoplasmic reticulum lumen	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0006457	Process	Protein folding	IBA
GO:0006457	Process	Protein folding	IEA
GO:0007283	Process	Spermatogenesis	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030246	Function	Carbohydrate binding	IEA
GO:0036503	Process	ERAD pathway	IBA
GO:0044183	Function	Protein folding chaperone	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051082	Function	Unfolded protein binding	IEA

Other IDs

• MIM: 611414
• HGNC: 20407
• e!Ensembl: ENSG00000269058

Protein

• UniProt ID: Q96L12
• Protein name: Calreticulin-3 (Calreticulin-2) (Calsperin)
• Protein function: During spermatogenesis, may act as a lectin-independent chaperone for specific client proteins such as ADAM3. Required for sperm fertility (By similarity). CALR3 capacity for calcium-binding may be absent or much lower than that of CALR. {ECO:00
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00262	Calreticulin	23 → 248	Calreticulin family	Family
  PF00262	Calreticulin	244 → 318	Calreticulin family	Family

• Tissue specificity: TISSUE SPECIFICITY: Testis specific. {ECO:0000269|PubMed:12384296}.
• Sequence:

  MARALVQLWAICMLRVALATVYFQEEFLDGEHWRNRWLQSTNDSRFGHFRLSSGKFYGHK
  EKDKGLQTTQNGRFYAISARFKPFSNKGKTLVIQYTVKHEQKMDCGGGYIKVFPADIDQK
  NLNGKSQYYIMFGPDICGFDIKKVHVILHFKNKYHENKKLIRCKVDGFTHLYTLILRPDL
  SYDVKIDGQSIESGSIEYDWNLTSLKKETSPAESKDWEQTKDNKAQDWEKHFLDASTSKQ
  SDWNGDLDGDWPAPMLQKPPYQDGLKPEGIHKDVWLHRKMKNTDYLTQYDLSEFENIGAI
  GLELWQVRSGTIFDNFLITDDEEYADNFGKATWGETKGPEREMDAIQAKEEMKKAREEEE
  EELLSGKINRHEHYFNQFHRRNEL

• Sequence length: 384

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Arrhythmogenic right ventricular cardiomyopathy	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CALR3-related disorder	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOMYOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiomyopathy	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOMYOPATHY, DILATED	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARDIOMYOPATHY, HYPERTROPHIC, FAMILIAL	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiovascular phenotype	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hypertrophic cardiomyopathy	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar ClinGen, Disgenet ClinGen, Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hypertrophic cardiomyopathy 19	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Primary dilated cardiomyopathy	Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Primary familial hypertrophic cardiomyopathy	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Restrictive cardiomyopathy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Cardiomyopathies	Cardiomyopathy	BEFREE	29988065		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cardiomyopathy Hypertrophic	Hypertrophic cardiomyopathy	Pubtator	22515980	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Familial Hypertrophic, 1 (disorder)	Cardiomyopathy	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	BEFREE	23578822		★☆☆☆☆ Found in Text Mining only
Hypertrophic Cardiomyopathy	Hypertrophic cardiomyopathy	CLINGEN_DG	17655857		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
NON RARE IN EUROPE: Familial isolated hypertrophic cardiomyopathy	Hypertrophic Cardiomyopathy	Orphanet			★☆☆☆☆ Found in Text Mining only
Testicular Neoplasms	Testicular neoplasm	Pubtator	26252478	Associate	★☆☆☆☆ Found in Text Mining only
Vitiligo	Vitiligo	BEFREE	31577462		★☆☆☆☆ Found in Text Mining only
VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding)	Vitiligo-associated SYSTEMIC LUPUS ERYTHEMATOSUS	BEFREE	31577462		★☆☆☆☆ Found in Text Mining only