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GeneBe

SEC24D

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

Basic information

Region (hg38): 4:118722822-118838683

Links

ENSG00000150961NCBI:9871OMIM:607186HGNC:10706Uniprot:O94855AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cole-Carpenter syndrome 2ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Dental; Musculoskeletal25683121; 26467156; 27942778; 30462379

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC24D gene.

  • not provided (367 variants)
  • Inborn genetic diseases (31 variants)
  • Cole-Carpenter syndrome 2 (20 variants)
  • not specified (5 variants)
  • SEC24D-related condition (2 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
60
clinvar
6
clinvar
66
missense
1
clinvar
1
clinvar
136
clinvar
12
clinvar
4
clinvar
154
nonsense
3
clinvar
3
clinvar
6
start loss
0
frameshift
6
clinvar
1
clinvar
1
clinvar
8
inframe indel
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
5
clinvar
5
splice region
7
8
7
22
non coding
4
clinvar
72
clinvar
44
clinvar
120
Total 10 11 144 144 54

Highest pathogenic variant AF is 0.0000329

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)1181948
4-118723512-CAATT-C Likely benign (Jan 28, 2023)1931835
4-118723540-T-C Uncertain significance (Sep 24, 2021)1525459
4-118723551-A-C Inborn genetic diseases Uncertain significance (Oct 10, 2023)3159337
4-118723555-A-T Uncertain significance (Aug 24, 2023)1396537
4-118723562-C-T Uncertain significance (Aug 04, 2023)1196804
4-118723566-A-G SEC24D-related condition Likely benign (Mar 20, 2019)3058562
4-118723565-C-CTT Uncertain significance (Feb 14, 2023)2575857
4-118723567-TAAG-T Uncertain significance (May 19, 2022)1987965
4-118723570-G-A Cole-Carpenter syndrome 2 Pathogenic (Oct 23, 2020)189339
4-118723573-G-A Uncertain significance (Jul 01, 2022)1959593
4-118723579-C-G Uncertain significance (Jul 06, 2022)1392819
4-118723580-C-T Uncertain significance (Aug 19, 2022)1444765
4-118723600-A-C Uncertain significance (Nov 19, 2023)1345860
4-118723602-C-G Likely benign (Sep 19, 2022)1547142
4-118723612-C-T Uncertain significance (Apr 26, 2022)1521240
4-118723621-A-G Uncertain significance (Jul 28, 2022)2180330
4-118723631-G-A Pathogenic (Jun 28, 2022)1381110
4-118723636-C-T Uncertain significance (Feb 05, 2022)1373110
4-118723637-G-A SEC24D-related condition Pathogenic/Likely pathogenic (Sep 22, 2023)2003692
4-118723649-T-C Inborn genetic diseases Uncertain significance (Feb 07, 2023)2481615
4-118723657-TA-T Uncertain significance (Aug 16, 2022)1442023
4-118723660-G-A Likely benign (Jan 24, 2018)714990
4-118723660-GA-G Benign (Sep 17, 2022)2052472
4-118723660-G-GA Cole-Carpenter syndrome 2 Benign (Jan 29, 2024)1283265

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC24Dprotein_codingprotein_codingENST00000280551 22115861
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.33e-71.001256730751257480.000298
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.434655600.8300.00002796744
Missense in Polyphen149216.160.68932606
Synonymous0.6641902020.9410.00001082018
Loss of Function3.972151.80.4050.00000269614

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001190.00119
Ashkenazi Jewish0.0002080.000198
East Asian0.0005810.000544
Finnish0.000.00
European (Non-Finnish)0.0002160.000211
Middle Eastern0.0005810.000544
South Asian0.00003300.0000327
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: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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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