• Gene id: 9871

Gene Summary

• Gene Symbol: SEC24D   Gene   UCSC   Ensembl
• Aliases: CLCRP2
• Gene name: SEC24 homolog D, COPII coat complex component
• Alternate names: protein transport protein Sec24D, SEC24 related gene family, member D, SEC24-related protein D,
• Gene location: 4q26 (118838682: 118722822)     Exons: 25     NC_000004.12
• Gene summary(Entrez): 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 f
• OMIM: 607186

SNPs

rs17840762

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000009.12   g.125241708G>A
NC_000009.11   g.128003987G>A
NG_027761.1   g.4680C>T
NG_063123.1   g.439G>A
XR_001746927.1   n.46G>A|SEQ=[G/A]|GENE=HSPA5
LOC107987127   107987127

rs17840761

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000009.12   g.125241700G>A
NC_000009.11   g.128003979G>A
NG_027761.1   g.4688C>T
NG_063123.1   g.431G>A
XR_001746927.1   n.38G>A|SEQ=[G/A]|GENE=HSPA5
LOC107987127   107987127

rs3216733

Strand:    Allele origin:   Allele change:   Mutation type: delins

NC_000009.12   g.125241516_125241517del
NC_000009.12   g.125241517del
NC_000009.12   g.125241517dup
NC_000009.12   g.125241516_125241517dup
NC_000009.11   g.128003795_128003796del
NC_000009.11   g.128003796del
NC_000009.11   g.128003796dup
NC_000009.11   g.128003795

Protein Summary

• Protein general information: O94855  
  • Name: Protein transport protein Sec24D (SEC24 related protein D)
  • Length: 1032  
  • Mass: 113010
  • Tissue specificity: Ubiquitously expressed, with higher amounts in placenta, pancreas, heart and liver. {ECO
• Sequence:

  MSQQGYVATPPYSQPQPGIGLSPPHYGHYGDPSHTASPTGMMKPAGPLGATATRGMLPPGPPPPGPHQFGQNGAH
  ATGHPPQRFPGPPPVNNVASSHAPYQPSAQSSYPGPISTSSVTQLGSQLSAMQINSYGSGMAPPSQGPPGPLSAT
  SLQTPPRPPQPSILQPGSQVLPPPPTTLNGPGASPLPLPMYRPDGLSGPPPPNAQYQPPPLPGQTLGAGYPPQQA
  NSGPQMAGAQLSYPGGFPGGPAQMAGPPQPQKKLDPDSIPSPIQVIENDRASRGGQVYATNTRGQIPPLVTTDCM
  IQDQGNASPRFIRCTTYCFPCTSDMAKQAQIPLAAVIKPFATIPSNESPLYLVNHGESGPVRCNRCKAYMCPFMQ
  FIEGGRRYQCGFCNCVNDVPPFYFQHLDHIGRRLDHYEKPELSLGSYEYVATLDYCRKSKPPNPPAFIFMIDVSY
  SNIKNGLVKLICEELKTMLEKIPKEEQEETSAIRVGFITYNKVLHFFNVKSNLAQPQMMVVTDVGEVFVPLLDGF
  LVNYQESQSVIHNLLDQIPDMFADSNENETVFAPVIQAGMEALKAADCPGKLFIFHSSLPTAEAPGKLKNRDDKK
  LVNTDKEKILFQPQTNVYDSLAKDCVAHGCSVTLFLFPSQYVDVASLGLVPQLTGGTLYKYNNFQMHLDRQQFLN
  DLRNDIEKKIGFDAIMRVRTSTGFRATDFFGGILMNNTTDVEMAAIDCDKAVTVEFKHDDKLSEDSGALIQCAVL
  YTTISGQRRLRIHNLGLNCSSQLADLYKSCETDALINFFAKSAFKAVLHQPLKVIREILVNQTAHMLACYRKNCA
  SPSAASQLILPDSMKVLPVYMNCLLKNCVLLSRPEISTDERAYQRQLVMTMGVADSQLFFYPQLLPIHTLDVKST
  MLPAAVRCSESRLSEEGIFLLANGLHMFLWLGVSSPPELIQGIFNVPSFAHINTDMTLLPEVGNPYSQQLRMIMG
  IIQQKRPYSMKLTIVKQREQPEMVFRQFLVEDKGLYGGSSYVDFLCCVHKEICQLLN

• Structural information:
  • Interpro: IPR029006  IPR007123  IPR036180  IPR006900  IPR036175   IPR006896  IPR012990  IPR041742  IPR036465  IPR006895  
  • CDD: cd01479
  • PDB: 3EFO 3EG9 5KYU 5KYW 5KYX 5KYY
  • PDBsum: 3EFO 3EG9 5KYU 5KYW 5KYX 5KYY
  • STRING: ENSP00000280551
• Other Databases: GeneCards:  SEC24D  Malacards:  SEC24D

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0008270	zinc ion binding	IDA	molecular function
GO:0090110	COPII-coated vesicle cargo loading	IDA	biological process
GO:0090110	COPII-coated vesicle cargo loading	IDA	biological process
GO:0030127	COPII vesicle coat	IDA	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	IMP	biological process
GO:0000149	SNARE binding	IPI	molecular function
GO:0000149	SNARE binding	IPI	molecular function
GO:0008270	zinc ion binding	IEA	molecular function
GO:0006886	intracellular protein transport	IEA	biological process
GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	IEA	biological process
GO:0030127	COPII vesicle coat	IEA	cellular component
GO:0046872	metal ion binding	IEA	molecular function
GO:0005783	endoplasmic reticulum	IEA	cellular component
GO:0031410	cytoplasmic vesicle	IEA	cellular component
GO:0016192	vesicle-mediated transport	IEA	biological process
GO:0005737	cytoplasm	IEA	cellular component
GO:0015031	protein transport	IEA	biological process
GO:0016020	membrane	IEA	cellular component
GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	TAS	biological process
GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	TAS	biological process
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	TAS	cellular component
GO:0048208	COPII vesicle coating	TAS	biological process
GO:0002474	antigen processing and presentation of peptide antigen via MHC class I	TAS	biological process
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005789	endoplasmic reticulum membrane	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005829	cytosol	TAS	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0001701	in utero embryonic development	IEA	biological process
GO:0005789	endoplasmic reticulum membrane	IEA	cellular component
GO:0012507	ER to Golgi transport vesicle membrane	IEA	cellular component
GO:0005829	cytosol	IEA	cellular component
GO:0043231	intracellular membrane-bounded organelle	IDA	cellular component
GO:0000139	Golgi membrane	IEA	cellular component
GO:0000139	Golgi membrane	IEA	cellular component
GO:0000139	Golgi membrane	IEA	cellular component
GO:0030127	COPII vesicle coat	NAS	cellular component
GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	NAS	biological process

KEGG pathways

Pathway id	Pathway name
hsa05130	Pathogenic Escherichia coli infection
hsa04141	Protein processing in endoplasmic reticulum

Diseases

Associated diseases	References
Cole-Carpenter syndrome	KEGG:H01572
Cole-Carpenter syndrome	KEGG:H01572
Aberrant CpGs in Low Motility Sperm	MIK: 21674046
Spermatogenic defects	MIK: 31037746
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			19 (6 controls, 13 cases)	Male infertility	GSE6872 analyzed by GEO2R (cutoff 1.5 fold)
21674046	Aberrant CpGs in Low Motility Sperm			18	Male infertility	GSE26881
31037746	Spermatogenic defects			16 (1 control, 15 cases)	Male infertility	GSE6023 analyzed using GEO2R