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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
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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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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)

Genotypes

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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