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    CAPN15 calpain 15 [ Homo sapiens (human) ]

    Gene ID: 6650, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CAPN15provided by HGNC
    Official Full Name
    calpain 15provided by HGNC
    Primary source
    HGNC:HGNC:11182
    See related
    Ensembl:ENSG00000103326 MIM:603267; AllianceGenome:HGNC:11182
    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
    OGIN; SOLH
    Summary
    This gene encodes a protein containing zinc-finger-like repeats and a calpain-like protease domain. The encoded protein may function as a transcription factor, RNA-binding protein, or in protein-protein interactions during visual system development. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in colon (RPKM 5.1), spleen (RPKM 4.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CAPN15 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (527712..554636)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (530789..558054)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (577712..604636)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RAB11 family interacting protein 3 Neighboring gene uncharacterized LOC107987417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:542303-542924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:544383-544961 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:544962-545539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:576271-576832 Neighboring gene long intergenic non-protein coding RNA 235 Neighboring gene microRNA 5587 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:595817-595984 Neighboring gene microRNA 3176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:610518-611064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:611065-611610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:614644-615540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:616436-617331 Neighboring gene proline rich 35 Neighboring gene NHL repeat containing 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Biallelic deletion in a minimal CAPN15 intron in siblings with a recognizable syndrome of congenital malformations and developmental delay. Mor-Shaked H, et al. Clin Genet, 2021 Apr. PMID 33410501
    2. Novel association of Dandy-Walker malformation with CAPN15 variants expands the phenotype of oculogastrointestinal neurodevelopmental syndrome. Beaman MM, et al. Am J Med Genet A, 2023 Nov. PMID 37596828, Free PMC Article
    3. SOLH, a human homologue of the Drosophila melanogaster small optic lobes gene is a member of the calpain and zinc-finger gene families and maps to human chromosome 16p13.3 near CATM (cataract with microphthalmia). Kamei M, et al. Genomics, 1998 Jul 15. PMID 9722942
    4. Biallelic variants in the small optic lobe calpain CAPN15 are associated with congenital eye anomalies, deafness and other neurodevelopmental deficits. Zha C, et al. Hum Mol Genet, 2020 Nov 4. PMID 32885237, Free PMC Article
    5. Sequencing analysis of forty-eight human image cDNA clones similar to Drosophila mutant protein. Volorio S, et al. DNA Seq, 1998. PMID 10524757

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel association of Dandy-Walker malformation with CAPN15 variants expands the phenotype of oculogastrointestinal neurodevelopmental syndrome.
      Title: Novel association of Dandy-Walker malformation with CAPN15 variants expands the phenotype of oculogastrointestinal neurodevelopmental syndrome.
    2. Biallelic deletion in a minimal CAPN15 intron in siblings with a recognizable syndrome of congenital malformations and developmental delay.
      Title: Biallelic deletion in a minimal CAPN15 intron in siblings with a recognizable syndrome of congenital malformations and developmental delay.
    3. Biallelic variants in the small optic lobe calpain CAPN15 are associated with congenital eye anomalies, deafness and other neurodevelopmental deficits.
      Title: Biallelic variants in the small optic lobe calpain CAPN15 are associated with congenital eye anomalies, deafness and other neurodevelopmental deficits.
    Submit: New GeneRIF Correction

    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

    Associated conditions

    Description Tests
    Oculogastrointestinal-neurodevelopmental syndrome
    MedGen: C5543355 OMIM: 619318 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
    EBI GWAS Catalog

    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

    Homology

    Clone Names

    • MGC131491

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium-dependent cysteine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in proteolysis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    calpain-15
    Names
    small optic lobes homolog

    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)

    1. NM_005632.3 → NP_005623.1  calpain-15

      See identical proteins and their annotated locations for NP_005623.1

      Status: REVIEWED

      Source sequence(s)
      Z97986, Z98882
      Consensus CDS
      CCDS10410.1
      UniProtKB/Swiss-Prot
      B1B1M4, O75808, Q2KHS2, Q8WTY9, Q9BUW0
      Related
      ENSP00000219611.2, ENST00000219611.7
      Conserved Domains (5) summary
      smart00547
      Location:5 → 29
      ZnF_RBZ; Zinc finger domain
      cd00044
      Location:476 → 791
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      sd00025
      Location:147 → 166
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      sd00029
      Location:344 → 363
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:412 → 438
      zf-RanBP; Zn-finger in Ran binding protein and others

    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

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      527712..554636
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434525.1 → XP_047290481.1  calpain-15 isoform X1

    2. XM_011522625.3 → XP_011520927.1  calpain-15 isoform X1

      See identical proteins and their annotated locations for XP_011520927.1

      Conserved Domains (4) summary
      smart00547
      Location:73 → 97
      ZnF_RBZ; Zinc finger domain
      cd00044
      Location:544 → 859
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      sd00025
      Location:169 → 191
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      sd00029
      Location:412 → 431
      zf-RanBP2; RanBP2-type Zn finger [structural motif]

    3. XM_011522631.3 → XP_011520933.1  calpain-15 isoform X4

      See identical proteins and their annotated locations for XP_011520933.1

      Conserved Domains (5) summary
      smart00547
      Location:5 → 29
      ZnF_RBZ; Zinc finger domain
      cd00044
      Location:476 → 791
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      sd00025
      Location:147 → 166
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      sd00029
      Location:344 → 363
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:412 → 438
      zf-RanBP; Zn-finger in Ran binding protein and others

    4. XM_047434533.1 → XP_047290489.1  calpain-15 isoform X5

      UniProtKB/Swiss-Prot
      B1B1M4, O75808, Q2KHS2, Q8WTY9, Q9BUW0

    5. XM_047434535.1 → XP_047290491.1  calpain-15 isoform X7

    6. XM_047434531.1 → XP_047290487.1  calpain-15 isoform X4

    7. XM_047434526.1 → XP_047290482.1  calpain-15 isoform X1

    8. XM_011522628.4 → XP_011520930.1  calpain-15 isoform X4

      See identical proteins and their annotated locations for XP_011520930.1

      Conserved Domains (5) summary
      smart00547
      Location:5 → 29
      ZnF_RBZ; Zinc finger domain
      cd00044
      Location:476 → 791
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      sd00025
      Location:147 → 166
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      sd00029
      Location:344 → 363
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:412 → 438
      zf-RanBP; Zn-finger in Ran binding protein and others

    9. XM_047434527.1 → XP_047290483.1  calpain-15 isoform X1

    10. XM_011522629.4 → XP_011520931.1  calpain-15 isoform X4

      See identical proteins and their annotated locations for XP_011520931.1

      Conserved Domains (5) summary
      smart00547
      Location:5 → 29
      ZnF_RBZ; Zinc finger domain
      cd00044
      Location:476 → 791
      CysPc; Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
      sd00025
      Location:147 → 166
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      sd00029
      Location:344 → 363
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam00641
      Location:412 → 438
      zf-RanBP; Zn-finger in Ran binding protein and others

    11. XM_047434528.1 → XP_047290484.1  calpain-15 isoform X1

    12. XM_047434529.1 → XP_047290485.1  calpain-15 isoform X2

    13. XM_047434532.1 → XP_047290488.1  calpain-15 isoform X4

    14. XM_047434530.1 → XP_047290486.1  calpain-15 isoform X3

    15. XM_047434534.1 → XP_047290490.1  calpain-15 isoform X6

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187610.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      130380..130698
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      530789..558054
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313766.1 → XP_054169741.1  calpain-15 isoform X2

    2. XM_054313769.1 → XP_054169744.1  calpain-15 isoform X3

    3. XM_054313762.1 → XP_054169737.1  calpain-15 isoform X1

    4. XM_054313772.1 → XP_054169747.1  calpain-15 isoform X4

    5. XM_054313763.1 → XP_054169738.1  calpain-15 isoform X1

    6. XM_054313773.1 → XP_054169748.1  calpain-15 isoform X4

    7. XM_054313760.1 → XP_054169735.1  calpain-15 isoform X1

    8. XM_054313759.1 → XP_054169734.1  calpain-15 isoform X1

    9. XM_054313764.1 → XP_054169739.1  calpain-15 isoform X1

    10. XM_054313767.1 → XP_054169742.1  calpain-15 isoform X2

    11. XM_054313774.1 → XP_054169749.1  calpain-15 isoform X4

    12. XM_054313765.1 → XP_054169740.1  calpain-15 isoform X1

    13. XM_054313771.1 → XP_054169746.1  calpain-15 isoform X4

    14. XM_054313775.1 → XP_054169750.1  calpain-15 isoform X5

      UniProtKB/Swiss-Prot
      B1B1M4, O75808, Q2KHS2, Q8WTY9, Q9BUW0

    15. XM_054313777.1 → XP_054169752.1  calpain-15 isoform X7

    16. XM_054313770.1 → XP_054169745.1  calpain-15 isoform X4

    17. XM_054313768.1 → XP_054169743.1  calpain-15 isoform X8

    18. XM_054313761.1 → XP_054169736.1  calpain-15 isoform X1

    19. XM_054313778.1 → XP_054169753.1  calpain-15 isoform X4

    20. XM_054313776.1 → XP_054169751.1  calpain-15 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75808.1 GenPept UniProtKB/Swiss-Prot:O75808

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