SEC24D
Basic information
Region (hg38): 4:118722822-118838683
Links
Phenotypes
GenCC
Source:
- Cole-Carpenter syndrome 2 (Moderate), mode of inheritance: AR
- Cole-Carpenter syndrome (Supportive), mode of inheritance: AD
- osteogenesis imperfecta type 1 (Supportive), mode of inheritance: AD
- Cole-Carpenter syndrome 2 (Moderate), mode of inheritance: AR
- epilepsy (Limited), mode of inheritance: AR
- Cole-Carpenter syndrome 2 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Cole-Carpenter syndrome 2 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dental; Musculoskeletal | 25683121; 26467156; 27942778; 30462379 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (11 variants)
- Cole-Carpenter syndrome 2 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC24D 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 | 83 | 89 | ||||
missense | 149 | 13 | 168 | |||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 8 | |||||
inframe indel | 5 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region | 7 | 11 | 8 | 26 | ||
non coding | 84 | 46 | 134 | |||
Total | 11 | 11 | 158 | 180 | 56 |
Highest pathogenic variant AF is 0.0000197
Variants in SEC24D
This is a list of pathogenic ClinVar variants found in the SEC24D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-118723343-T-C | Likely benign (May 18, 2019) | |||
4-118723512-CAATT-C | Likely benign (Jan 28, 2023) | |||
4-118723540-T-C | Inborn genetic diseases | Uncertain significance (May 15, 2024) | ||
4-118723551-A-C | Inborn genetic diseases | Uncertain significance (Oct 10, 2023) | ||
4-118723555-A-T | Uncertain significance (Aug 24, 2023) | |||
4-118723562-C-T | Uncertain significance (Aug 04, 2023) | |||
4-118723566-A-G | SEC24D-related disorder | Likely benign (Mar 20, 2019) | ||
4-118723565-C-CTT | Uncertain significance (Feb 14, 2023) | |||
4-118723567-TAAG-T | Uncertain significance (May 19, 2022) | |||
4-118723570-G-A | Cole-Carpenter syndrome 2 | Pathogenic (Oct 23, 2020) | ||
4-118723573-G-A | Uncertain significance (Jul 01, 2022) | |||
4-118723579-C-G | Uncertain significance (Jul 06, 2022) | |||
4-118723580-C-T | Uncertain significance (Aug 19, 2022) | |||
4-118723600-A-C | Uncertain significance (Nov 19, 2023) | |||
4-118723602-C-G | Likely benign (Sep 19, 2022) | |||
4-118723612-C-T | Uncertain significance (Apr 26, 2022) | |||
4-118723621-A-G | Uncertain significance (Jul 28, 2022) | |||
4-118723631-G-A | Pathogenic (Jun 28, 2022) | |||
4-118723636-C-T | Uncertain significance (Feb 05, 2022) | |||
4-118723637-G-A | SEC24D-related disorder | Pathogenic/Likely pathogenic (Sep 22, 2023) | ||
4-118723649-T-C | Inborn genetic diseases | Uncertain significance (Feb 07, 2023) | ||
4-118723657-TA-T | Uncertain significance (Aug 16, 2022) | |||
4-118723660-G-A | Likely benign (Jan 24, 2018) | |||
4-118723660-GA-G | Benign (Sep 17, 2022) | |||
4-118723660-G-GA | Cole-Carpenter syndrome 2 | Benign (Jan 29, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SEC24D | protein_coding | protein_coding | ENST00000280551 | 22 | 115861 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.33e-7 | 1.00 | 125673 | 0 | 75 | 125748 | 0.000298 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.43 | 465 | 560 | 0.830 | 0.0000279 | 6744 |
Missense in Polyphen | 149 | 216.16 | 0.6893 | 2606 | ||
Synonymous | 0.664 | 190 | 202 | 0.941 | 0.0000108 | 2018 |
Loss of Function | 3.97 | 21 | 51.8 | 0.405 | 0.00000269 | 614 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00119 | 0.00119 |
Ashkenazi Jewish | 0.000208 | 0.000198 |
East Asian | 0.000581 | 0.000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000216 | 0.000211 |
Middle Eastern | 0.000581 | 0.000544 |
South Asian | 0.0000330 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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:17499046, PubMed:20427317, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24C 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: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
- 0.124
Intolerance Scores
- loftool
- 0.443
- rvis_EVS
- 1.18
- rvis_percentile_EVS
- 92.84
Haploinsufficiency Scores
- pHI
- 0.691
- hipred
- Y
- hipred_score
- 0.593
- ghis
- 0.444
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.757
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec24d
- 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
- sec24d
- Affected structure
- chondrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- undifferentiated
Gene ontology
- Biological process
- in utero embryonic development;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