mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for SEC24D

Gene summary

Basic gene Info.	Gene symbol	SEC24D
	Gene name	SEC24 family member D
	Synonyms	-
	Cytomap	UCSC genome browser: 4q26
	Type of gene	protein-coding
	RefGenes	NM_014822.2,
	Description	SEC24 family, member DSEC24 related gene family, member DSEC24-related protein Dprotein transport protein Sec24D
	Modification date	20141207
dbXrefs	MIM : 607186
	HGNC : HGNC
	Ensembl : ENSG00000150961
	HPRD : 06218
	Vega : OTTHUMG00000132957
Protein	UniProt: O94855 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SEC24D
	BioGPS: 9871
Pathway	NCI Pathway Interaction Database: SEC24D
	KEGG: SEC24D
	REACTOME: SEC24D
	Pathway Commons: SEC24D
Context	iHOP: SEC24D
	ligand binding site mutation search in PubMed: SEC24D
	UCL Cancer Institute: SEC24D
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID

GO Term

PubMed ID

Top

Ligand binding site mutations for SEC24D

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
C388	C388S	BRCA	1
Y820	Y820H	COAD	1
Y820	R821Q	UCEC	1
S831	A830T	UCEC	1

cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

Top

Protein structure related information for SEC24D

Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
(ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)

: nsSNV at non-LBS

: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.

LBS	AAchange of nsSNV	Relative stability change
C388	C388S	-1.3094971
Y820	R821Q	-1.1510826
Y820	Y820H	-1.0868062
S831	A830T	-0.90031089

(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for SEC24D from PDB

Top

Differential gene expression and gene-gene network for SEC24D

Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)

* Left PPI network was created from samples with mutations in the LBS of SEC24D and the right PPI network was created from samples without mutations in the LBS of SEC24D. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

Top

Phenotype information for SEC24D

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

Top

Pharmacological information for SEC24D

Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.