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

Gene ID: 9871, updated on 2-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
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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 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
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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

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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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

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