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    SEC24D SEC24 homolog D, COPII coat complex component [ Homo sapiens (human) ]

    Gene ID: 9871, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SEC24Dprovided by HGNC
    Official Full Name
    SEC24 homolog D, COPII coat complex componentprovided by HGNC
    Primary source
    HGNC:HGNC:10706
    See related
    Ensembl:ENSG00000150961 MIM:607186; AllianceGenome:HGNC:10706
    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
    CLCRP2
    Summary
    The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
    Expression
    Ubiquitous expression in thyroid (RPKM 21.6), small intestine (RPKM 18.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEC24D in Genome Data Viewer
    Location:
    4q26
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (118722823..118836126, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (122028139..122141474, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (119643978..119757281, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900768 Neighboring gene METTL14 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21849 Neighboring gene methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119756637-119757528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15653 Neighboring gene uncharacterized LOC105377393 Neighboring gene synaptopodin 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:119838359-119838859 Neighboring gene uncharacterized LOC105377394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21851

    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
    • 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. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Curtis SW, et al. Hum Genet, 2023 Oct. PMID 37676273
    2. Mutations in the carboxyl-terminal SEC24 binding motif of the serotonin transporter impair folding of the transporter. El-Kasaby A, et al. J Biol Chem, 2010 Dec 10. PMID 20889976, Free PMC Article
    3. Mutations in SEC24D, encoding a component of the COPII machinery, cause a syndromic form of osteogenesis imperfecta. Garbes L, et al. Am J Hum Genet, 2015 Mar 5. PMID 25683121, Free PMC Article
    4. Novel mutations in the SEC24D gene in Chinese families with autosomal recessive osteogenesis imperfecta. Zhang H, et al. Osteoporos Int, 2017 Apr. PMID 27942778
    5. Identification and characterization of SEC24D as a susceptibility gene for hepatitis B virus infection. Jiang X, et al. Sci Rep, 2019 Sep 17. PMID 31530870, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes.
      Title: Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes.
    2. Identification and characterization of SEC24D as a susceptibility gene for hepatitis B virus infection.
      Title: Identification and characterization of SEC24D as a susceptibility gene for hepatitis B virus infection.
    3. ERp29 as a regulator of Insulin biosynthesis.
      Title: ERp29 as a regulator of Insulin biosynthesis.
    4. The study found missense mutations in the SEC24D gene in Chinese families with autosomal recessive osteogenesis imperfect.
      Title: Novel mutations in the SEC24D gene in Chinese families with autosomal recessive osteogenesis imperfecta.
    5. three mutant SEC24D alleles in a rare autosomal-recessively inherited skeletal disorder characterized by pre- and postnatal bone fragility, skull ossification defects, craniofacial dysmorphism, and short stature
      Title: Mutations in SEC24D, encoding a component of the COPII machinery, cause a syndromic form of osteogenesis imperfecta.
    6. A triple arg motif mediates alpha(2B)-adrenergic receptor interaction with Sec24C/D and export
      Title: A triple arg motif mediates α(2B)-adrenergic receptor interaction with Sec24C/D and export.
    7. Mutations in the carboxyl-terminal SEC24 binding motif of the serotonin transporter impair folding of the transporter
      Title: Mutations in the carboxyl-terminal SEC24 binding motif of the serotonin transporter impair folding of the transporter.
    8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
    10. concentrative endoplasmic reticulum-export is contingent on a direct interaction of GAT1 with Sec24D.
      Title: Concentrative export from the endoplasmic reticulum of the gamma-aminobutyric acid transporter 1 requires binding to SEC24D.
    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
    Cole-Carpenter syndrome 2
    MedGen: C4225382 OMIM: 616294 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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ43974, KIAA0755

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNARE binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in COPII-coated vesicle cargo loading IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in COPII-coated vesicle cargo loading IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of COPII vesicle coat IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of COPII vesicle coat IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of COPII vesicle coat NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in ER to Golgi transport vesicle membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in endoplasmic reticulum exit site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    protein transport protein Sec24D
    Names
    SEC24 related gene family, member D
    SEC24-related protein D

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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

    1. NG_042032.1 RefSeqGene

      Range
      5046..118349
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318066.2 → NP_001304995.1  protein transport protein Sec24D isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is one amino acid longer than isoform 1.
      Source sequence(s)
      AF130464, BC035761, DA034453
      UniProtKB/TrEMBL
      A8K6V0
      Conserved Domains (2) summary
      cl26464
      Location:8 → 294
      Atrophin-1; Atrophin-1 family
      cl27110
      Location:182 → 1028
      zf-Sec23_Sec24; Sec23/Sec24 zinc finger

    2. NM_014822.4 → NP_055637.2  protein transport protein Sec24D isoform 1

      See identical proteins and their annotated locations for NP_055637.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).
      Source sequence(s)
      AB018298, AK291765, BC035761, DB224337
      Consensus CDS
      CCDS3710.1
      UniProtKB/Swiss-Prot
      O94855, Q8IYI7
      UniProtKB/TrEMBL
      A8K6V0
      Related
      ENSP00000280551.6, ENST00000280551.11
      Conserved Domains (2) summary
      pfam09606
      Location:1 → 256
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      cl27110
      Location:132 → 1027
      zf-Sec23_Sec24; Sec23/Sec24 zinc finger

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      118722823..118836126 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      122028139..122141474 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O94855.2 GenPept UniProtKB/Swiss-Prot:O94855

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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