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GeneBe

SEC24C

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

Basic information

Region (hg38): 10:73744371-73772161

Links

ENSG00000176986NCBI:9632OMIM:607185HGNC:10705Uniprot:P53992AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC24C gene.

  • Inborn genetic diseases (31 variants)
  • not provided (9 variants)

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
clinvar
2
clinvar
5
missense
30
clinvar
1
clinvar
1
clinvar
32
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
1
clinvar
1
Total 0 0 30 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)2623939
10-73746963-A-G not specified Uncertain significance (Nov 17, 2023)3159305
10-73751219-C-G not specified Uncertain significance (Apr 07, 2022)2282390
10-73751227-A-G not specified Uncertain significance (Dec 15, 2023)3159318
10-73759630-G-A not specified Uncertain significance (Sep 28, 2022)2400186
10-73759735-C-A not specified Uncertain significance (Jan 22, 2024)3159323
10-73759743-C-G not specified Uncertain significance (Sep 14, 2023)2624143
10-73759752-G-A not specified Uncertain significance (Aug 23, 2021)2380866
10-73759776-T-C not specified Likely benign (Apr 18, 2023)2517203
10-73760027-C-T not specified Uncertain significance (Jan 02, 2024)3159324
10-73760062-T-A not specified Uncertain significance (Jun 22, 2021)2350830
10-73760078-C-G not specified Uncertain significance (Nov 08, 2022)2375254
10-73760147-G-A not specified Uncertain significance (Dec 17, 2023)3159325
10-73760299-C-G Benign (Apr 04, 2018)718500
10-73760307-C-G Benign (Dec 31, 2019)771741
10-73760396-T-G Benign (Dec 31, 2019)782290
10-73760734-G-T not specified Uncertain significance (Sep 16, 2021)2249967
10-73760803-A-C not specified Uncertain significance (Feb 15, 2023)2459236
10-73765544-G-A not specified Uncertain significance (Oct 17, 2023)3159306
10-73765550-A-G not specified Uncertain significance (Oct 13, 2021)2373518
10-73765553-C-T not specified Uncertain significance (Jan 06, 2023)2455621
10-73765902-T-C not specified Uncertain significance (Mar 08, 2024)3159307
10-73766089-A-G not specified Uncertain significance (Sep 14, 2022)2378290
10-73766103-C-A Microcephaly Uncertain significance (-)813708
10-73766132-T-C not specified Uncertain significance (Jul 06, 2021)2235031

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC24Cprotein_codingprotein_codingENST00000339365 2227800
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000003711257380101257480.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.505176220.8310.00003467029
Missense in Polyphen180265.590.677733076
Synonymous-0.5292512411.040.00001272294
Loss of Function6.21452.60.07600.00000269595

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004640.0000462
European (Non-Finnish)0.00006190.0000615
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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