SEC24A

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

Basic information

Region (hg38): 5:134648784-134727909

Links

ENSG00000113615 ∙ NCBI:10802 ∙ OMIM:607183 ∙ HGNC:10703 ∙ Uniprot:O95486 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			43			43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	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)
5-134661216-G-T		not specified	Uncertain significance (Jan 24, 2024)
5-134661224-A-G		not specified	Uncertain significance (Sep 16, 2021)
5-134661277-C-G		not specified	Uncertain significance (Oct 05, 2023)
5-134661299-C-G		not specified	Uncertain significance (Aug 14, 2023)
5-134661343-A-G		not specified	Uncertain significance (Nov 20, 2023)
5-134661373-A-C		not specified	Uncertain significance (Aug 09, 2021)
5-134661422-C-A		not specified	Uncertain significance (Sep 06, 2022)
5-134661437-A-C		not specified	Uncertain significance (May 26, 2022)
5-134661491-C-A		not specified	Uncertain significance (Jan 20, 2023)
5-134661524-C-A		not specified	Uncertain significance (May 16, 2022)
5-134666874-C-T		not specified	Uncertain significance (Feb 28, 2024)
5-134666879-G-C		not specified	Uncertain significance (Dec 12, 2023)
5-134666901-C-T		not specified	Uncertain significance (Oct 05, 2021)
5-134666915-C-T		not specified	Uncertain significance (Aug 30, 2022)
5-134671820-A-G		not specified	Uncertain significance (May 04, 2022)
5-134671859-G-A		not specified	Uncertain significance (Jun 21, 2022)
5-134674651-G-A		not specified	Uncertain significance (Nov 15, 2021)
5-134675143-G-A		not specified	Uncertain significance (Oct 29, 2021)
5-134675148-C-T		not specified	Uncertain significance (Nov 03, 2023)
5-134676037-C-T		not specified	Uncertain significance (Dec 12, 2023)
5-134676082-A-C		not specified	Uncertain significance (Aug 17, 2021)
5-134679689-A-T		not specified	Uncertain significance (Aug 20, 2023)
5-134682375-C-T		not specified	Uncertain significance (Jun 27, 2023)
5-134686808-C-A		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC24A	protein_coding	protein_coding	ENST00000398844	23	79035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.77e-9	1.00	124743	0	54	124797	0.000216

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.406	551	578	0.953	0.0000288	7047
Missense in Polyphen		118	141.85	0.83185		1666
Synonymous	-0.557	222	212	1.05	0.0000108	2230
Loss of Function	4.12	24	57.8	0.415	0.00000302	688

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000350	0.000350
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000278	0.000278
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000241	0.000230
Middle Eastern	0.000278	0.000278
South Asian	0.000320	0.000294
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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