CAPN6 calpain 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CAPN6provided by HGNC
Official Full Name: calpain 6provided by HGNC
Primary source: HGNC:HGNC:1483
See related: Ensembl:ENSG00000077274 MIM:300146; AllianceGenome:HGNC:1483
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: CANPX; CAPNX; CalpM; DJ914P14.1
Summary: Calpains are ubiquitous, well-conserved family of calcium-dependent, cysteine proteases. The calpain proteins are heterodimers consisting of an invariant small subunit and variable large subunits. The large subunit possesses a cysteine protease domain, and both subunits possess calcium-binding domains. Calpains have been implicated in neurodegenerative processes, as their activation can be triggered by calcium influx and oxidative stress. The protein encoded by this gene is highly expressed in the placenta. Its C-terminal region lacks any homology to the calmodulin-like domain of other calpains. The protein lacks critical active site residues and thus is suggested to be proteolytically inactive. The protein may play a role in tumor formation by inhibiting apoptosis and promoting angiogenesis. [provided by RefSeq, Nov 2009]
Expression: Biased expression in placenta (RPKM 59.5), endometrium (RPKM 13.7) and 5 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq23

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (111245099..111270483, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (109693306..109718689, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (110488327..110513711, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Advanced glycation end products promote the progression of chronic kidney diseases by targeting calpain 6.
Title: Advanced glycation end products promote the progression of chronic kidney diseases by targeting calpain 6.
A calpain-6/YAP axis in sarcoma stem cells that drives the outgrowth of tumors and metastases.
Title: A calpain-6/YAP axis in sarcoma stem cells that drives the outgrowth of tumors and metastases.
The investigation of calpain in human placenta with fetal growth restriction.
Title: The investigation of calpain in human placenta with fetal growth restriction.
CAPN6 Regulates Uterine Leiomyoma Cell Proliferation and Apoptosis through the Rac1-Dependent Signaling Pathway.
Title: CAPN6 Regulates Uterine Leiomyoma Cell Proliferation and Apoptosis through the Rac1-Dependent Signaling Pathway.
Non-proteolytic calpain-6 interacts with VEGFA and promotes angiogenesis by increasing VEGF secretion.
Title: Non-proteolytic calpain-6 interacts with VEGFA and promotes angiogenesis by increasing VEGF secretion.
High CAPN6 expression is associated with liver cancer.
Title: miR-449a promotes liver cancer cell apoptosis by downregulation of Calpain 6 and POU2F1.
CAPN6 promotes atherogenicity in inflamed macrophages by disturbing CWC22/EJC systems.
Title: Calpain-6 confers atherogenicity to macrophages by dysregulating pre-mRNA splicing.
syndecan-2 exerts its pro-apoptotic function through modulation of the endothelin-1/NFkappaB signaling and through downregulation of calpain-6.
Title: Calpain-6 is an endothelin-1 signaling dependent protective factor in chemoresistant osteosarcoma.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Family-based association study for bipolar affective disorder.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of calpain 6 (CAPN6) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

DXS1252 (e-PCR)
- UniSTS:99347

AL023597 (e-PCR)
- UniSTS:1052

AL032604 (e-PCR)
- UniSTS:93282

SGC32977 (e-PCR)
- UniSTS:71051

DXS7540 (e-PCR)
- UniSTS:153842

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables calcium-dependent cysteine-type endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables microtubule binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in microtubule bundle formation	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in proteolysis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in spindle microtubule	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: calpain-6

Names: calpain-like protease X-linked; calpamodulin

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.

Genomic

NG_015962.2 RefSeqGene

Range

5000..30384

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_014289.4 → NP_055104.2 calpain-6

See identical proteins and their annotated locations for NP_055104.2

Status: REVIEWED

Source sequence(s)

AL031117

Consensus CDS

CCDS14555.1

UniProtKB/Swiss-Prot

D3DUY7, Q9UEQ1, Q9UJA8, Q9Y6Q1

UniProtKB/TrEMBL

B2R6T2

Related

ENSP00000317214.1, ENST00000324068.2

Conserved Domains (3) summary

smart00230
Location:13 → 351

CysPc; Calpain-like thiol protease family

cd04046
Location:514 → 639

C2_Calpain; C2 domain present in Calpain proteins

cd00214
Location:349 → 497

Calpain_III; Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are ...