GCA grancalcin [Homo sapiens (human)] - Gene

Summary

Official Symbol: GCAprovided by HGNC
Official Full Name: grancalcinprovided by HGNC
Primary source: HGNC:HGNC:15990
See related: Ensembl:ENSG00000115271 MIM:607030; AllianceGenome:HGNC:15990
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GCL
Summary: This gene encodes a calcium-binding protein that is abundant in neutrophils and macrophages. In the absence of divalent cation, this protein localizes to the cytosolic fraction; with magnesium alone, it partitions with the granule fraction; and in the presence of magnesium and calcium, it associates with both the granule and membrane fractions. Alternative splicing and use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Aug 2016]
Expression: Broad expression in bone marrow (RPKM 47.3), appendix (RPKM 18.4) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q24.2

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (162318763..162375396)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (162775430..162833885)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (163175273..163219633)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GCA activates TRAF6 ubiquitin ligase activity to induce Lys63 ubiquitination of ULK1, a crucial regulator of autophagy, resulting in its stabilization and activation. It was also highlighted the role of GCA-TRAF6-ULK1 autophagy regulatory axis in imatinib resistance.
Title: GCA links TRAF6-ULK1-dependent autophagy activation in resistant chronic myeloid leukemia.
Results indicate that heterodimerization of GCA and TLR9 is important for TLR9-mediated downstream signaling and might serve to fine tune processes against viral infection.
Title: Grancalcin (GCA) modulates Toll-like receptor 9 (TLR9) mediated signaling through its direct interaction with TLR9.
IFIH1-GCA-KCNH7 locus is not associated with genetic susceptibility to multiple sclerosis in French patients
Title: IFIH1-GCA-KCNH7 locus is not associated with genetic susceptibility to multiple sclerosis in French patients.
IFIH1 interferon induced helicase, GCA grancalcin or the potassium channel KCNH7 - are potential candidates implicated in the pathogenesis of multiple sclerosis.
Title: IFIH1-GCA-KCNH7 locus: influence on multiple sclerosis risk.
The reported type 1 diabetes association is from a linkage disequilibrium region including three candidate genes, FAP, IFIH1 and GCA.
Title: The association between the IFIH1 locus and type 1 diabetes.
Observational study of gene-disease association. (HuGE Navigator)
Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
GCA interacts with SRI in vivo and in vitro.
Title: The PEF family proteins sorcin and grancalcin interact in vivo and in vitro.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH1483 (e-PCR)
- UniSTS:32791

GCA__6795 (e-PCR)
- UniSTS:466202

D2S2559 (e-PCR)
- UniSTS:43038

D2S1927E (e-PCR)
- UniSTS:147326

RH36533 (e-PCR)
- UniSTS:28132

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in membrane fusion	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in azurophil granule lumen	TAS Traceable Author Statement more info
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: grancalcin

Names: grancalcin, EF-hand calcium-binding protein; grancalcin, penta-EF-hand protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001330265.1 → NP_001317194.1 grancalcin isoform a

Status: REVIEWED

Source sequence(s)

AC010876

Conserved Domains (2) summary

pfam13499
Location:140 → 195

EF-hand_7; EF-hand domain pair

cl08302
Location:79 → 134

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_001330266.1 → NP_001317195.1 grancalcin isoform a

Status: REVIEWED

Source sequence(s)

AC010876

Conserved Domains (2) summary

pfam13499
Location:140 → 195

EF-hand_7; EF-hand domain pair

cl08302
Location:79 → 134

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_001330267.1 → NP_001317196.1 grancalcin isoform a

Status: REVIEWED

Source sequence(s)

AC010876

Conserved Domains (2) summary

pfam13499
Location:140 → 195

EF-hand_7; EF-hand domain pair

cl08302
Location:79 → 134

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_001330268.1 → NP_001317197.1 grancalcin isoform c

Status: REVIEWED

Source sequence(s)

AC010876

Conserved Domains (2) summary

pfam13499
Location:151 → 206

EF-hand_7; EF-hand domain pair

cl08302
Location:90 → 145

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_001330270.2 → NP_001317199.1 grancalcin isoform d

Status: REVIEWED

Source sequence(s)

AC010876

Consensus CDS

CCDS82527.1

UniProtKB/TrEMBL

H7BXD5

Conserved Domains (2) summary

pfam13499
Location:106 → 161

EF-hand_7; EF-hand domain pair

cl08302
Location:45 → 100

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_001330271.2 → NP_001317200.1 grancalcin isoform d

Status: REVIEWED

Source sequence(s)

AC010876, AK295413, BI760070

Consensus CDS

CCDS82527.1

UniProtKB/TrEMBL

H7BXD5

Related

ENSP00000233612.4, ENST00000233612.8

Conserved Domains (2) summary

pfam13499
Location:106 → 161

EF-hand_7; EF-hand domain pair

cl08302
Location:45 → 100

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
NM_012198.5 → NP_036330.1 grancalcin isoform b

See identical proteins and their annotated locations for NP_036330.1

Status: REVIEWED

Source sequence(s)

AC010876, BC005214, M81637

Consensus CDS

CCDS2218.1

UniProtKB/Swiss-Prot

B2R5X3, P28676, Q53TB5, Q59EP3

Related

ENSP00000394842.2, ENST00000437150.7

Conserved Domains (1) summary

cd16186
Location:53 → 217

EFh_PEF_grancalcin; Penta-EF hand, calcium binding motifs, found in grancalcin

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

162318763..162375396

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006712398.5 → XP_006712461.1 grancalcin isoform X1

Conserved Domains (2) summary

pfam13499
Location:151 → 206

EF-hand_7; EF-hand domain pair

cl08302
Location:90 → 145

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
XM_006712400.5 → XP_006712463.1 grancalcin isoform X2

Conserved Domains (2) summary

cd15897
Location:68 → 96

EFh_PEF; EF-hand motif [structural motif]

cl25352
Location:68 → 224

EFh_PEF; The penta-EF hand (PEF) family
XM_047443881.1 → XP_047299837.1 grancalcin isoform X2
XM_047443882.1 → XP_047299838.1 grancalcin isoform X2
XM_005246446.4 → XP_005246503.1 grancalcin isoform X3

Conserved Domains (2) summary

pfam13499
Location:125 → 180

EF-hand_7; EF-hand domain pair

cl08302
Location:64 → 119

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
XM_017003767.2 → XP_016859256.1 grancalcin isoform X4

Conserved Domains (2) summary

pfam13499
Location:106 → 161

EF-hand_7; EF-hand domain pair

cl08302
Location:45 → 100

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
XM_011510926.3 → XP_011509228.1 grancalcin isoform X4

Conserved Domains (2) summary

pfam13499
Location:106 → 161

EF-hand_7; EF-hand domain pair

cl08302
Location:45 → 100

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
XM_011510928.3 → XP_011509230.1 grancalcin isoform X5

UniProtKB/TrEMBL

H7C2Z6

Related

ENSP00000408620.1, ENST00000414723.1

Conserved Domains (1) summary

cl08302
Location:1 → 52

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...