SEC24C

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

Basic information

Region (hg38): 10:73744371-73772161

Links

ENSG00000176986 ∙ NCBI:9632 ∙ OMIM:607185 ∙ HGNC:10705 ∙ Uniprot:P53992 ∙ 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 SEC24C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC24C 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				3	2	5
missense			48	1	1	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	0	48	4	4

Variants in SEC24C

This is a list of pathogenic ClinVar variants found in the SEC24C region.

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

Position	Type	Phenotype	Significance	ClinVar
10-73746872-G-C		not specified	Uncertain significance (Sep 14, 2023)
10-73746963-A-G		not specified	Uncertain significance (Nov 17, 2023)
10-73751219-C-G		not specified	Uncertain significance (Apr 07, 2022)
10-73751227-A-G		not specified	Uncertain significance (Dec 15, 2023)
10-73759630-G-A		not specified	Uncertain significance (Sep 28, 2022)
10-73759735-C-A		not specified	Uncertain significance (Jan 22, 2024)
10-73759743-C-G		not specified	Uncertain significance (Sep 14, 2023)
10-73759752-G-A		not specified	Uncertain significance (Aug 23, 2021)
10-73759776-T-C		not specified	Likely benign (Apr 18, 2023)
10-73760027-C-T		not specified	Uncertain significance (Jan 02, 2024)
10-73760062-T-A		not specified	Uncertain significance (Jun 22, 2021)
10-73760078-C-G		not specified	Uncertain significance (Nov 08, 2022)
10-73760147-G-A		not specified	Uncertain significance (Dec 17, 2023)
10-73760299-C-G			Benign (Apr 04, 2018)
10-73760307-C-G			Benign (Dec 31, 2019)
10-73760396-T-G			Benign (Dec 31, 2019)
10-73760734-G-T		not specified	Uncertain significance (Sep 16, 2021)
10-73760803-A-C		not specified	Uncertain significance (Feb 15, 2023)
10-73765544-G-A		not specified	Uncertain significance (Oct 17, 2023)
10-73765550-A-G		not specified	Uncertain significance (Oct 13, 2021)
10-73765553-C-T		not specified	Uncertain significance (Jan 06, 2023)
10-73765902-T-C		not specified	Uncertain significance (Mar 08, 2024)
10-73766089-A-G		not specified	Uncertain significance (Sep 14, 2022)
10-73766103-C-A		Microcephaly	Uncertain significance (-)
10-73766132-T-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC24C	protein_coding	protein_coding	ENST00000339365	22	27800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000371	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	517	622	0.831	0.0000346	7029
Missense in Polyphen		180	265.59	0.67773		3076
Synonymous	-0.529	251	241	1.04	0.0000127	2294
Loss of Function	6.21	4	52.6	0.0760	0.00000269	595

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

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:10214955, PubMed:17499046, PubMed:18843296, PubMed:20427317). Plays a central role in cargo selection within the COPII complex and together with SEC24D may have a different specificity compared to SEC24A and SEC24B (PubMed:17499046, PubMed:20427317, PubMed:18843296). May more specifically package GPI-anchored proteins through the cargo receptor TMED10 (PubMed:20427317). May also be specific for IxM motif-containing cargos like the SNAREs GOSR2 and STX5 (PubMed:18843296). {ECO:0000269|PubMed:10214955, 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;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: 0.0953

Intolerance Scores

• loftool: 0.158
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.98

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.696
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec24c
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype

Zebrafish Information Network

• Gene name: sec24c
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased length

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;COPII vesicle coating;COPII-coated vesicle cargo loading
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;COPII vesicle coat
• Molecular function: SNARE binding;protein binding;zinc ion binding