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GeneBe

SEC24A

SEC24 homolog A, COPII coat complex component, the group of COPII coat complex

Basic information

Region (hg38): 5:134648784-134727909

Links

ENSG00000113615NCBI:10802OMIM:607183HGNC:10703Uniprot:O95486AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC24A gene.

  • Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC24A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
28
clinvar
28
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 28 0 0

Variants in SEC24A

This is a list of pathogenic ClinVar variants found in the SEC24A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
5-134649171-A-G not specified Uncertain significance (Jun 11, 2021)2362201
5-134661216-G-T not specified Uncertain significance (Jan 24, 2024)3159271
5-134661224-A-G not specified Uncertain significance (Sep 16, 2021)2357125
5-134661277-C-G not specified Uncertain significance (Oct 05, 2023)3159272
5-134661299-C-G not specified Uncertain significance (Aug 14, 2023)2618403
5-134661343-A-G not specified Uncertain significance (Nov 20, 2023)3159278
5-134661373-A-C not specified Uncertain significance (Aug 09, 2021)2409396
5-134661422-C-A not specified Uncertain significance (Sep 06, 2022)2310105
5-134661437-A-C not specified Uncertain significance (May 26, 2022)2291080
5-134661491-C-A not specified Uncertain significance (Jan 20, 2023)2477015
5-134661524-C-A not specified Uncertain significance (May 16, 2022)2289949
5-134666874-C-T not specified Uncertain significance (Feb 28, 2024)3159280
5-134666879-G-C not specified Uncertain significance (Dec 12, 2023)3159281
5-134666901-C-T not specified Uncertain significance (Oct 05, 2021)2400329
5-134666915-C-T not specified Uncertain significance (Aug 30, 2022)2224323
5-134671820-A-G not specified Uncertain significance (May 04, 2022)2287205
5-134671859-G-A not specified Uncertain significance (Jun 21, 2022)2296098
5-134674651-G-A not specified Uncertain significance (Nov 15, 2021)2355317
5-134675143-G-A not specified Uncertain significance (Oct 29, 2021)3159266
5-134675148-C-T not specified Uncertain significance (Nov 03, 2023)3159267
5-134676037-C-T not specified Uncertain significance (Dec 12, 2023)3159268
5-134676082-A-C not specified Uncertain significance (Aug 17, 2021)2246396
5-134679689-A-T not specified Uncertain significance (Aug 20, 2023)2619700
5-134682375-C-T not specified Uncertain significance (Jun 27, 2023)2589741
5-134686808-C-A not specified Uncertain significance (Apr 08, 2022)2212233

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC24Aprotein_codingprotein_codingENST00000398844 2379035
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.77e-91.001247430541247970.000216
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4065515780.9530.00002887047
Missense in Polyphen118141.850.831851666
Synonymous-0.5572222121.050.00001082230
Loss of Function4.122457.80.4150.00000302688

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003500.000350
Ashkenazi Jewish0.0002990.000298
East Asian0.0002780.000278
Finnish0.0001390.000139
European (Non-Finnish)0.0002410.000230
Middle Eastern0.0002780.000278
South Asian0.0003200.000294
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules for their transport to the Golgi complex (PubMed:20427317, PubMed:17499046, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24B may have a different specificity compared to SEC24C and SEC24D. May package preferentially cargos with cytoplasmic DxE or LxxLE motifs and may also recognize conformational epitopes (PubMed:17499046, PubMed:18843296). {ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296, ECO:0000269|PubMed:20427317}.;
Pathway
Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Immune System;Adaptive Immune System;Class I MHC mediated antigen processing & presentation;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC (Consensus)

Recessive Scores

pRec
0.0997

Intolerance Scores

loftool
0.355
rvis_EVS
-1.06
rvis_percentile_EVS
7.55

Haploinsufficiency Scores

pHI
0.198
hipred
Y
hipred_score
0.516
ghis
0.579

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.814

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sec24a
Phenotype
liver/biliary system phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process
antigen processing and presentation of peptide antigen via MHC class I;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;cholesterol homeostasis;regulation of low-density lipoprotein particle receptor biosynthetic process;COPII vesicle coating;positive regulation of protein secretion;COPII-coated vesicle cargo loading
Cellular component
Golgi membrane;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;COPII vesicle coat
Molecular function
protein binding;zinc ion binding