Seroatlas · Human Serome Atlas

SEC24D

Protein transport protein Sec24D

Also known as: KIAA0755, SC24D_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O94855
Gene: SEC24D
Ensembl: ENSG00000150961
Chromosome: 4
Canonical length: 1032 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Vesicles

OverviewNCBI Gene

The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

Canonical amino-acid sequenceUniProt

1032 residues, UniProt reviewed canonical sequence.

>O94855|SEC24D
     1  MSQQGYVATP PYSQPQPGIG LSPPHYGHYG DPSHTASPTG MMKPAGPLGA TATRGMLPPG
    61  PPPPGPHQFG QNGAHATGHP PQRFPGPPPV NNVASSHAPY QPSAQSSYPG PISTSSVTQL
   121  GSQLSAMQIN SYGSGMAPPS QGPPGPLSAT SLQTPPRPPQ PSILQPGSQV LPPPPTTLNG
   181  PGASPLPLPM YRPDGLSGPP PPNAQYQPPP LPGQTLGAGY PPQQANSGPQ MAGAQLSYPG
   241  GFPGGPAQMA GPPQPQKKLD PDSIPSPIQV IENDRASRGG QVYATNTRGQ IPPLVTTDCM
   301  IQDQGNASPR FIRCTTYCFP CTSDMAKQAQ IPLAAVIKPF ATIPSNESPL YLVNHGESGP
   361  VRCNRCKAYM CPFMQFIEGG RRYQCGFCNC VNDVPPFYFQ HLDHIGRRLD HYEKPELSLG
   421  SYEYVATLDY CRKSKPPNPP AFIFMIDVSY SNIKNGLVKL ICEELKTMLE KIPKEEQEET
   481  SAIRVGFITY NKVLHFFNVK SNLAQPQMMV VTDVGEVFVP LLDGFLVNYQ ESQSVIHNLL
   541  DQIPDMFADS NENETVFAPV IQAGMEALKA ADCPGKLFIF HSSLPTAEAP GKLKNRDDKK
   601  LVNTDKEKIL FQPQTNVYDS LAKDCVAHGC SVTLFLFPSQ YVDVASLGLV PQLTGGTLYK
   661  YNNFQMHLDR QQFLNDLRND IEKKIGFDAI MRVRTSTGFR ATDFFGGILM NNTTDVEMAA
   721  IDCDKAVTVE FKHDDKLSED SGALIQCAVL YTTISGQRRL RIHNLGLNCS SQLADLYKSC
   781  ETDALINFFA KSAFKAVLHQ PLKVIREILV NQTAHMLACY RKNCASPSAA SQLILPDSMK
   841  VLPVYMNCLL KNCVLLSRPE ISTDERAYQR QLVMTMGVAD SQLFFYPQLL PIHTLDVKST
   901  MLPAAVRCSE SRLSEEGIFL LANGLHMFLW LGVSSPPELI QGIFNVPSFA HINTDMTLLP
   961  EVGNPYSQQL RMIMGIIQQK RPYSMKLTIV KQREQPEMVF RQFLVEDKGL YGGSSYVDFL
  1021  CCVHKEICQL LN

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SEC24D can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Other membrane
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.34
Highest tissue expression: 49 nTPM

Expression across tissuesHPA

Tissue

liver: 49 nTPM
cervix: 46 nTPM
blood vessel: 42 nTPM
smooth muscle: 39 nTPM
small intestine: 38 nTPM
duodenum: 35 nTPM

Single-cell type

somatotrophs: 414 nCPM
plasma cells: 395 nCPM
gonadotrophs: 360 nCPM
lactotrophs: 336 nCPM
pancreatic islet cells: 244 nCPM
endometrial stromal cells: 233 nCPM

Immune cell

eosinophil: 16 nTPM
non-classical monocyte: 7.5 nTPM
MAIT T-cell: 6.3 nTPM
intermediate monocyte: 6 nTPM
basophil: 5.9 nTPM
myeloid DC: 5.8 nTPM

Brain region

cerebral cortex: 17 nTPM
hypothalamus: 16 nTPM
choroid plexus: 15 nTPM
basal ganglia: 11 nTPM
white matter: 11 nTPM
midbrain: 11 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SEC24D.

Disease | AllUniProt

Conditions SEC24D is implicated in, by any mechanism.

Cole-Carpenter syndrome 2 (CLCRP2) MIM:616294

Disease | GeneticClinVar

42 pathogenic / likely-pathogenic of 623 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Cole-Carpenter syndrome 2
Inborn genetic diseases
SEC24D-related disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.58
gnomAD pLI: 0
gnomAD missense Z: 1.43
DepMap mean gene effect: 0.06
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SEC24D in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SEC24D as an antibody target. Whether an autoantibody or antibody against SEC24D could matter depends on whether native SEC24D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SEC24D is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label SEC24D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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