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

Summary

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

Location:: 4q26

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (118722823..118836126, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (122028139..122141474, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (119643978..119757281, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
ERp29 as a regulator of Insulin biosynthesis.
Title: ERp29 as a regulator of Insulin biosynthesis.
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.
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.
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.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH104321 (e-PCR)
- UniSTS:98646

SHGC-50671 (e-PCR)
- UniSTS:46973

D4S2788 (e-PCR)
- UniSTS:46974

D4S2565E (e-PCR)
- UniSTS:150975

SHGC-36538 (e-PCR)
- UniSTS:34275

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

NG_042032.1 RefSeqGene

Range

5046..118349

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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