CAPN10 calpain 10 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CAPN10provided by HGNC
Official Full Name: calpain 10provided by HGNC
Primary source: HGNC:HGNC:1477
See related: Ensembl:ENSG00000142330 MIM:605286; AllianceGenome:HGNC:1477
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: CANP10; NIDDM1
Summary: Calpains represent a 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 catalytic subunit has four domains: domain I, the N-terminal regulatory domain that is processed upon calpain activation; domain II, the protease domain; domain III, a linker domain of unknown function; and domain IV, the calmodulin-like calcium-binding domain. This gene encodes a large subunit. It is an atypical calpain in that it lacks the calmodulin-like calcium-binding domain and instead has a divergent C-terminal domain. It is similar in organization to calpains 5 and 6. This gene is associated with type 2 or non-insulin-dependent diabetes mellitus (NIDDM), and is located within the NIDDM1 region. Multiple alternative transcript variants have been described for this gene. [provided by RefSeq, Sep 2010]
Expression: Ubiquitous expression in spleen (RPKM 8.4), testis (RPKM 6.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (240586734..240599104)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (241080759..241093164)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (241526151..241538521)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Molecular role of non-exonic variants in CALPAIN 10 gene in polycystic ovarian syndrome in Saudi women.
Title: Molecular role of non-exonic variants in CALPAIN 10 gene in polycystic ovarian syndrome in Saudi women.
Correlation between TCF7L2 and CAPN10 gene polymorphisms and gestational diabetes mellitus in different geographical regions: a meta-analysis.
Title: Correlation between TCF7L2 and CAPN10 gene polymorphisms and gestational diabetes mellitus in different geographical regions: a meta-analysis.
Dysregulated miRNA-375, IL-17, TGF-beta, and Microminerals Are Associated with Calpain-10 SNP 19 in Diabetic Patients: Correlation with Diabetic Nephropathy Stages.
Title: Dysregulated miRNA-375, IL-17, TGF-β, and Microminerals Are Associated with Calpain-10 SNP 19 in Diabetic Patients: Correlation with Diabetic Nephropathy Stages.
Identification of DNA methylation of CAPN10 gene changes in the patients with type 2 diabetes mellitus as a predictive biomarker instead of HbA1c, random blood sugar, lipid profile, kidney function test, and some risk factors.
Title: Identification of DNA methylation of CAPN10 gene changes in the patients with type 2 diabetes mellitus as a predictive biomarker instead of HbA1c, random blood sugar, lipid profile, kidney function test, and some risk factors.
Clinical significance of sHER2ECD and calpain10 expression in tumor tissues of patients with breast cancer.
Title: Clinical significance of sHER2‑ECD and calpain‑10 expression in tumor tissues of patients with breast cancer.
The GSTT1 null genotype frequency is associated with hyperglycemia in type 2 diabetes mellitus, whereas there is no difference in the CAPN10 SNP19 in this condition.
Title: GSTT1, Calpain 10 SNP 19 and indices of glycaemia in type 2 diabetes.
grade B and grade D diabetes in the CC and TC genotypes of rs2975760 were significantly different from those in the TT genotype.Grade B and grade D diabetes in the AA and AG genotypes of rs3792267 were significantly different compared with those in the GG genotype (P<0.05), and allele A was significantly increased compared with allele G (P<0.05).
Title: The Association Between the rs2975760 and rs3792267 Single Nucleotide Polymorphisms of Calpain 10 (CAPN10) and Gestational Diabetes Mellitus.
Calpain-10 regulates actin dynamics by proteolysis of microtubule-associated protein 1B
Title: Calpain-10 regulates actin dynamics by proteolysis of microtubule-associated protein 1B.
This study provides evidence that SNP43 (G/A) in the CAPN10 gene increases the risk of cognitive impairment in cerebral small vessel disease patients.
Title: The SNP43 (G/A) polymorphism in CAPN10 gene confers an increased risk of cognitive impairment in cerebral small vessel disease.
The 3R/3R genotype of the indel-19 variant of the CAPN-10 gene influenced increased glucose levels in these Mexican women with gestational diabetes mellitus.
Title: Association analysis of calpain 10 gene variants/haplotypes with gestational diabetes mellitus among Mexican women.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Diabetes mellitus, noninsulin-dependent, 1 MedGen: C1832544 OMIM: 601283 GeneReviews: Not available	Compare labs

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

WI-15718 (e-PCR)
- UniSTS:13585

G31184 (e-PCR)
- UniSTS:181844

G31185 (e-PCR)
- UniSTS:181845

G31186 (e-PCR)
- UniSTS:181846

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNARE binding	ISS Inferred from Sequence or Structural Similarity more info
enables calcium-dependent cysteine-type endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium-dependent cysteine-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables cytoskeletal protein 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 cellular component disassembly involved in execution phase of apoptosis	IC Inferred by Curator more info
involved_in cellular response to insulin stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of D-glucose import	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of insulin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of intracellular transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of type B pancreatic cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in proteolysis	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteolysis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in type B pancreatic cell apoptotic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: calpain-10

Names: calcium-activated neutral proteinase 10; calpain-like protease CAPN10

NP_075571.2

EC 3.4.22.-

EC 3.4.22.17

NP_075573.3

EC 3.4.22.-

EC 3.4.22.17

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_011558.3 RefSeqGene

Range

5002..17372

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_023083.4 → NP_075571.2 calpain-10 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as CAPN10a) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AC124862

Consensus CDS

CCDS42838.1

UniProtKB/Swiss-Prot

A8MVS7, Q4ZFV1, Q8NCD4, Q96IG4, Q96JI2, Q9HC89, Q9HC90, Q9HC91, Q9HC92, Q9HC93, Q9HC94, Q9HC95, Q9HC96

UniProtKB/TrEMBL

B7WPF5

Related

ENSP00000375844.2, ENST00000391984.7

Conserved Domains (2) summary

cd00044
Location:2 → 319

CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.

cd00214
Location:335 → 496

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 ...
NM_023085.4 → NP_075573.3 calpain-10 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3, also known as CAPN10c) lacks two consecutive exons, resulting in the loss of an in-frame segment in the 3' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.

Source sequence(s)

AC124862

Consensus CDS

CCDS33420.1

UniProtKB/TrEMBL

B7Z6G3

Related

ENSP00000270362.6, ENST00000354082.8

Conserved Domains (2) summary

cd00044
Location:2 → 319

CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.

cd00214
Location:335 → 498

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 ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

240586734..240599104

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

241080759..241093164

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_021251.3: Suppressed sequence

Description

NM_021251.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
NM_023084.1: Suppressed sequence

Description

NM_023084.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
NM_023086.1: Suppressed sequence

Description

NM_023086.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
NM_023087.1: Suppressed sequence

Description

NM_023087.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
NM_023088.1: Suppressed sequence

Description

NM_023088.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
NM_023089.1: Suppressed sequence

Description

NM_023089.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.