Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	3208
Gene name	Hippocalcin
Gene symbol	HPCA
Synonyms (NCBI Gene)	BDR2DYT2
Chromosome	1
Chromosome location	1p35.1
Summary	The protein encoded by this gene is a member of neuron-specific calcium-binding proteins family found in the retina and brain. This protein is associated with the plasma membrane. It has similarities to proteins located in the photoreceptor cells that reg

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs550921485	G>A	Pathogenic	Missense variant, coding sequence variant
rs775863165	C>A,T	Pathogenic	Coding sequence variant, missense variant
rs786205675	C>A	Pathogenic	Missense variant, coding sequence variant

Show/Hide all (28)

miRTarBase ID	miRNA	Experiments	Reference
MIRT736027	hsa-miR-24-3p	Luciferase reporter assayWestern blottingImmunofluorescenceqRT-PCR	31486848
MIRT1053972	hsa-miR-1321	CLIP-seq
MIRT1053973	hsa-miR-24	CLIP-seq
MIRT1053974	hsa-miR-3144-5p	CLIP-seq
MIRT1053975	hsa-miR-3157-5p	CLIP-seq
MIRT1053976	hsa-miR-3179	CLIP-seq
MIRT1053977	hsa-miR-3202	CLIP-seq
MIRT1053978	hsa-miR-4283	CLIP-seq
MIRT1053979	hsa-miR-4419a	CLIP-seq
MIRT1053980	hsa-miR-4437	CLIP-seq
MIRT1053981	hsa-miR-4476	CLIP-seq
MIRT1053982	hsa-miR-4510	CLIP-seq
MIRT1053983	hsa-miR-4691-3p	CLIP-seq
MIRT1053984	hsa-miR-4716-3p	CLIP-seq
MIRT1053985	hsa-miR-4728-5p	CLIP-seq
MIRT1053986	hsa-miR-4739	CLIP-seq
MIRT1053987	hsa-miR-4756-5p	CLIP-seq
MIRT2012248	hsa-miR-1909	CLIP-seq
MIRT2244632	hsa-miR-1260	CLIP-seq
MIRT2244633	hsa-miR-1260b	CLIP-seq
MIRT2244634	hsa-miR-188-3p	CLIP-seq
MIRT2244635	hsa-miR-3156-3p	CLIP-seq
MIRT1053978	hsa-miR-4283	CLIP-seq
MIRT1053984	hsa-miR-4716-3p	CLIP-seq
MIRT2389150	hsa-miR-1275	CLIP-seq
MIRT2389151	hsa-miR-4665-5p	CLIP-seq
MIRT2451358	hsa-miR-637	CLIP-seq
MIRT2451359	hsa-miR-661	CLIP-seq

Show/Hide all (36)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003779	Function	Actin binding	IDA	11964161
GO:0005509	Function	Calcium ion binding	IBA
GO:0005509	Function	Calcium ion binding	IDA	28398555
GO:0005509	Function	Calcium ion binding	IEA
GO:0005509	Function	Calcium ion binding	NAS	8387172
GO:0005515	Function	Protein binding	IPI	32296183, 33961781
GO:0005737	Component	Cytoplasm	IDA	28398555
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0009966	Process	Regulation of signal transduction	IBA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	ISS
GO:0019722	Process	Calcium-mediated signaling	IEA
GO:0019900	Function	Kinase binding	IEA
GO:0030424	Component	Axon	IEA
GO:0032590	Component	Dendrite membrane	IEA
GO:0032809	Component	Neuronal cell body membrane	IEA
GO:0032839	Component	Dendrite cytoplasm	IEA
GO:0042802	Function	Identical protein binding	IDA	28398555
GO:0043204	Component	Perikaryon	IEA
GO:0044327	Component	Dendritic spine head	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048839	Process	Inner ear development	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:0071257	Process	Cellular response to electrical stimulus	IEA
GO:0071277	Process	Cellular response to calcium ion	IMP	28398555
GO:0090314	Process	Positive regulation of protein targeting to membrane	IEA
GO:0098794	Component	Postsynapse	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099149	Process	Regulation of postsynaptic neurotransmitter receptor internalization	IEA
GO:1901385	Process	Regulation of voltage-gated calcium channel activity	IMP	28398555
GO:1901986	Process	Response to ketamine	IEA
GO:1902065	Process	Response to L-glutamate	IEA
GO:1904010	Process	Response to Aroclor 1254	IEA
GO:1905232	Process	Cellular response to L-glutamate	IEA

MIM	HGNC	e!Ensembl
142622	5144	ENSG00000121905

P84074

Protein name

Neuron-specific calcium-binding protein hippocalcin (Calcium-binding protein BDR-2)

Protein function

Calcium-binding protein that may play a role in the regulation of voltage-dependent calcium channels (PubMed:28398555). May also play a role in cyclic-nucleotide-mediated signaling through the regulation of adenylate and guanylate cyclases (By s

PDB

5G4P , 5G58 , 5M6C , 7OWM

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13833	EF-hand_8	39 → 90	EF-hand domain pair	Domain
PF13499	EF-hand_7	98 → 174	EF-hand domain pair	Domain
PF00036	EF-hand_1	148 → 176	EF hand	Domain

Tissue specificity

TISSUE SPECIFICITY: Brain specific. {ECO:0000269|PubMed:8166736}.

Sequence

MGKQNSKLRPEMLQDLRENTEFSELELQEWYKGFLKDCPTGILNVDEFKKIYANFFPYGD
ASKFAEHVFRTFDTNSDGTIDFREFIIALSVTSRGRLEQKLMWAFSMYDLDGNGYISREE
MLEIVQAIYKMVSSVMKMPEDESTPEKRTEKIFRQMDTNNDGKLSLEEFIRGAKSDPSIV
RLLQCDPSSASQF

Sequence length

193

Interactions

View interactions

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)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Torsion dystonia 2	Pathogenic	rs786205675, rs775863165	RCV000170352 RCV000170353	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
COMPLEX MOVEMENT DISORDER WITH OR WITHOUT NEURODEVELOPMENTAL FEATURES	—	ClinGen, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA 2, TORSION, AUTOSOMAL RECESSIVE	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA MUSCULORUM DEFORMANS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA MUSCULORUM DEFORMANS TYPE 2	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL TORSION DYSTONIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GENETIC TORSION DYSTONIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HPCA-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC FAMILIAL DYSTONIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY DYSTONIA, DYT2 TYPE	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (19)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Blepharospasm	Blepharospasm	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	22696308		★★★★★ ★☆☆☆☆ Found in Text Mining only
Deglutition Disorders	Dysphagia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dystonia	Dystonia	Pubtator	28398555	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
DYSTONIA 2, TORSION, AUTOSOMAL RECESSIVE (disorder)	Dystonia	UNIPROT_DG	25799108, 28398555		★★★★★ ★☆☆☆☆ Found in Text Mining only
DYSTONIA 2, TORSION, AUTOSOMAL RECESSIVE (disorder)	Dystonia	GENOMICS_ENGLAND_DG	25799108, 30145809		★★★★★ ★☆☆☆☆ Found in Text Mining only
DYSTONIA 2, TORSION, AUTOSOMAL RECESSIVE (disorder)	Dystonia	ORPHANET_DG	25799108		★★★★★ ★☆☆☆☆ Found in Text Mining only
DYSTONIA 2, TORSION, AUTOSOMAL RECESSIVE (disorder)	Dystonia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
DYSTONIA 2, TORSION, AUTOSOMAL RECESSIVE (disorder)	Dystonia	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dystonia Disorders	Dystonia	BEFREE	15390074, 25799108, 26991507, 27771228, 28398555, 30145809, 31301343		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dystonia Musculorum Deformans	Dystonia	BEFREE	14694054		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dystonia Musculorum Deformans	Dystonia	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dystonic Disorders	Dystonia	Pubtator	25799108, 28398555	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Early onset torsion dystonia	Dystonia	BEFREE	12194383, 14694054		★★★★★ ★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington Disease	BEFREE	19686238		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	10100726		★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary dystonia, DYT2 type	Dystonia	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Severe Combined Immunodeficiency	Severe combined immunodeficiency disease	BEFREE	10100726		★★★★★ ★☆☆☆☆ Found in Text Mining only

HPCA (hippocalcin)