SEC22A

Summary

SEC22A (SEC22 homolog A, vesicle trafficking protein, HGNC:20260) is a protein-coding gene on chromosome 3q21.1, encoding Vesicle-trafficking protein SEC22a (Q96IW7). May be involved in vesicle transport between the ER and the Golgi complex.

The protein encoded by this gene belongs to the member of the SEC22 family of vesicle trafficking proteins. This protein has similarity to rat SEC22 and may act in the early stages of the secretory pathway.

Source: NCBI Gene 26984 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_012430

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20260
Approved symbol	SEC22A
Name	SEC22 homolog A, vesicle trafficking protein
Location	3q21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000121542
Ensembl biotype	protein_coding
OMIM	612442
Entrez	26984

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 20 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000309934, ENST00000466519, ENST00000466950, ENST00000473494, ENST00000477063, ENST00000480631, ENST00000481965, ENST00000487572, ENST00000491366, ENST00000492595, ENST00000908419, ENST00000908421, ENST00000908422, ENST00000908423, ENST00000908424, ENST00000916521, ENST00000916522, ENST00000916523, ENST00000916524, ENST00000916525, ENST00000945893, ENST00000945894

RefSeq mRNA: 1 — MANE Select: NM_012430 NM_012430

CCDS: CCDS3021

Canonical transcript exons

ENST00000492595 — 7 exons

Exon	Start	End
ENSE00000823786	123245899	123246014
ENSE00001938820	123271522	123274136
ENSE00001943940	123201943	123201986
ENSE00003493274	123259524	123259589
ENSE00003501929	123225103	123225297
ENSE00003553502	123209199	123209399
ENSE00003640550	123223559	123223722

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 92.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.3347 / max 143.5361, expressed in 1793 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38277	14.5983	1787
38278	0.7363	271

Top tissues by expression

278 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	92.43	gold quality
oocyte	CL:0000023	92.30	gold quality
calcaneal tendon	UBERON:0003701	91.81	gold quality
islet of Langerhans	UBERON:0000006	89.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.94	gold quality
left testis	UBERON:0004533	86.21	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.14	gold quality
right testis	UBERON:0004534	85.85	gold quality
testis	UBERON:0000473	85.26	gold quality
ventricular zone	UBERON:0003053	84.68	gold quality
adrenal tissue	UBERON:0018303	84.63	gold quality
ganglionic eminence	UBERON:0004023	84.15	gold quality
stromal cell of endometrium	CL:0002255	83.72	gold quality
skin of abdomen	UBERON:0001416	83.58	gold quality
skin of leg	UBERON:0001511	83.58	gold quality
popliteal artery	UBERON:0002250	83.37	gold quality
tibial artery	UBERON:0007610	83.36	gold quality
gall bladder	UBERON:0002110	83.34	gold quality
rectum	UBERON:0001052	83.29	gold quality
pancreas	UBERON:0001264	83.08	gold quality
smooth muscle tissue	UBERON:0001135	83.00	gold quality
lower esophagus mucosa	UBERON:0035834	82.99	gold quality
monocyte	CL:0000576	82.97	gold quality
right coronary artery	UBERON:0001625	82.74	gold quality
esophagus mucosa	UBERON:0002469	82.68	gold quality
aorta	UBERON:0000947	82.65	gold quality
leukocyte	CL:0000738	82.63	gold quality
descending thoracic aorta	UBERON:0002345	82.46	gold quality
mononuclear cell	CL:0000842	82.42	gold quality
cortical plate	UBERON:0005343	82.22	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

123 targeting SEC22A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515

Literature-anchored findings (GeneRIF, showing 1)

• The 200 kDa crystal structure of Sec22 bound to Sec23/24 reveals that the transport signal is a folded epitope rather than a conventional short peptide sequence. (PMID:17499046)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	sec22a	ENSDARG00000078328
mus_musculus	Sec22a	ENSMUSG00000034473
rattus_norvegicus	Sec22a	ENSRNOG00000043069
drosophila_melanogaster	Syb	FBGN0003660
caenorhabditis_elegans		WBGENE00004898
caenorhabditis_elegans		WBGENE00004899
caenorhabditis_elegans		WBGENE00014084
caenorhabditis_elegans		WBGENE00044062

Paralogs (10): VAMP3 (ENSG00000049245), SEC22C (ENSG00000093183), YKT6 (ENSG00000106636), VAMP4 (ENSG00000117533), VAMP8 (ENSG00000118640), VAMP7 (ENSG00000124333), VAMP1 (ENSG00000139190), VAMP5 (ENSG00000168899), VAMP2 (ENSG00000220205), SEC22B (ENSG00000265808)

Protein

Protein identifiers

Vesicle-trafficking protein SEC22a — Q96IW7 (reviewed: Q96IW7)

Alternative names: SEC22 vesicle-trafficking protein homolog A, SEC22 vesicle-trafficking protein-like 2

All UniProt accessions (8): C9J463, C9JDJ8, C9JNZ0, C9JR77, C9JRY4, C9JZ27, F8WAU7, Q96IW7

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in vesicle transport between the ER and the Golgi complex.

Subcellular location. Endoplasmic reticulum membrane.

Similarity. Belongs to the synaptobrevin family.

RefSeq proteins (1): NP_036562* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010908	Longin_dom	Domain
IPR011012	Longin-like_dom_sf	Homologous_superfamily
IPR043546	Sec22a/c	Family
IPR059071	SEC22a-c_C	Domain

Pfam: PF13774, PF25970

UniProt features (19 total): topological domain 5, sequence conflict 4, transmembrane region 4, modified residue 3, initiator methionine 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96IW7-F1	83.00	0.51

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 2, 6, 8

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-204005	COPII-mediated vesicle transport
R-HSA-199977	ER to Golgi Anterograde Transport
R-HSA-199991	Membrane Trafficking
R-HSA-392499	Metabolism of proteins
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-5653656	Vesicle-mediated transport
R-HSA-597592	Post-translational protein modification
R-HSA-948021	Transport to the Golgi and subsequent modification

MSigDB gene sets: 97 (showing top): GOBP_MEMBRANE_FUSION, GOBP_VESICLE_MEDIATED_TRANSPORT, RIZKI_TUMOR_INVASIVENESS_3D_DN, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, BLALOCK_ALZHEIMERS_DISEASE_UP, KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, chr3q21, GOBP_MEMBRANE_ORGANIZATION, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, GOBP_GOLGI_VESICLE_TRANSPORT, GOMF_SNAP_RECEPTOR_ACTIVITY, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION

GO Biological Process (5): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein transport (GO:0015031), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), vesicle-mediated transport (GO:0016192), membrane fusion (GO:0061025)

GO Molecular Function (2): SNAP receptor activity (GO:0005484), protein binding (GO:0005515)

GO Cellular Component (7): endoplasmic reticulum membrane (GO:0005789), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), endomembrane system (GO:0012505), membrane (GO:0016020), melanosome (GO:0042470)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Membrane Trafficking	1
Transport to the Golgi and subsequent modification	1
Vesicle-mediated transport	1
Post-translational protein modification	1
Metabolism of proteins	1
Asparagine N-linked glycosylation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
cellular anatomical structure	3
Golgi vesicle transport	2
transport	2
endomembrane system	2
intracellular membrane-bounded organelle	2
intercellular transport	1
intracellular transport	1
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
membrane organization	1
protein-macromolecule adaptor activity	1
membrane fusion	1
fusogenic activity	1
binding	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1
pigment granule	1

Protein interactions and networks

STRING

1454 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SEC22A	BET1	O15155	953
SEC22A	GOSR2	O14653	924
SEC22A	STX5	Q13190	877
SEC22A	VTI1B	Q9UEU0	846
SEC22A	GOSR1	O95249	696
SEC22A	SCFD1	Q8WVM8	692
SEC22A	BET1L	Q9NYM9	691
SEC22A	GORASP2	Q9H8Y8	554
SEC22A	YKT6	O15498	532
SEC22A	GOLGA2	Q08379	522
SEC22A	TRMO	Q9BU70	484
SEC22A	ARFIP1	P53367	460
SEC22A	GOLPH3	Q9H4A6	457
SEC22A	TRAPPC5	Q8IUR0	451
SEC22A	TANGO2	Q6ICL3	432

IntAct

363 interactions, top by confidence:

A	B	Type	Score
MSR1	SEC22A	psi-mi:“MI:0915”(physical association)	0.780
SEC22A	DTX2	psi-mi:“MI:0915”(physical association)	0.780
DTX2	SEC22A	psi-mi:“MI:0915”(physical association)	0.780
SEC22A	EDA	psi-mi:“MI:0915”(physical association)	0.780
TMEM79	SEC22A	psi-mi:“MI:0915”(physical association)	0.780
SEC22A	MSR1	psi-mi:“MI:0915”(physical association)	0.780
EDA	SEC22A	psi-mi:“MI:0915”(physical association)	0.780
SEC22A	TMEM79	psi-mi:“MI:0915”(physical association)	0.780
SEC22A	ERLIN1	psi-mi:“MI:0915”(physical association)	0.720
SFTPC	SEC22A	psi-mi:“MI:0915”(physical association)	0.720
STX4	SEC22A	psi-mi:“MI:0915”(physical association)	0.720
FATE1	SEC22A	psi-mi:“MI:0915”(physical association)	0.720
SEC22A	SFTPC	psi-mi:“MI:0915”(physical association)	0.720
SEC22A	STX4	psi-mi:“MI:0915”(physical association)	0.720
SEC22A	FATE1	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (145): SEC22A (Two-hybrid), SEC22A (Two-hybrid), SEC22A (Two-hybrid), SEC22A (Two-hybrid), SEC22A (Two-hybrid), SEC22A (Two-hybrid), TMEM79 (Two-hybrid), FATE1 (Two-hybrid), DTX2 (Two-hybrid), SYNE4 (Two-hybrid), SEC22A (Affinity Capture-MS), SEC22A (Two-hybrid), SEC22A (Affinity Capture-MS), SEC22A (Affinity Capture-MS), SEC22A (Affinity Capture-MS)

ESM2 similar proteins: A7RVK7, A7TNS4, B4IB36, B4QL99, C0HLF1, C0Z274, C1C4M3, C5DJG1, F4JPP0, O02173, O13732, O43032, O74942, P0C1J0, P12868, P29551, P32613, P32910, P32916, P38247, P38334, P53129, P53237, Q03630, Q03784, Q08972, Q10150, Q21045, Q28HU2, Q29NZ8, Q4R866, Q4S4I5, Q54CA7, Q54DY3, Q54IQ5, Q54ZR7, Q5FV35, Q5ZKP4, Q642F4, Q6FU19

Diamond homologs: O08547, O08595, O75396, P22214, Q4KM74, Q4R866, Q5RAI9, Q5ZJW4, Q642F4, Q6C880, Q6CJA0, Q6FWT0, Q6P7L4, Q74ZD2, Q7SXP0, Q7ZV15, Q8BH47, Q8BXT9, Q94AU2, Q96IW7, Q9BRL7, Q9Y7L0, O70404, Q3T0Y8, Q5REQ5, Q9BV40, Q9WUF4, Q2YDJ2, O60073, P36015, Q6FW27, Q3T000

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

49 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1266 predictions. Top by Δscore:

Variant	Effect	Δscore
3:123209396:T:G	donor_gain	1.0000
3:123209396:T:TG	donor_gain	1.0000
3:123209400:G:GG	donor_gain	1.0000
3:123223557:A:AG	acceptor_gain	1.0000
3:123223558:G:GG	acceptor_gain	1.0000
3:123223558:GTTTT:G	acceptor_gain	1.0000
3:123223636:T:TA	acceptor_gain	1.0000
3:123223637:G:A	acceptor_gain	1.0000
3:123223719:TTTGG:T	donor_loss	1.0000
3:123223720:TTGGT:T	donor_loss	1.0000
3:123223723:G:GT	donor_loss	1.0000
3:123223724:T:TC	donor_loss	1.0000
3:123225100:T:G	acceptor_gain	1.0000
3:123245894:TCCA:T	acceptor_loss	1.0000
3:123245895:CCA:C	acceptor_loss	1.0000
3:123245896:CAGCT:C	acceptor_loss	1.0000
3:123245897:A:AC	acceptor_loss	1.0000
3:123245897:A:AG	acceptor_gain	1.0000
3:123245898:G:GA	acceptor_gain	1.0000
3:123245898:G:GC	acceptor_loss	1.0000
3:123259518:TTGCA:T	acceptor_loss	1.0000
3:123259519:TGCA:T	acceptor_loss	1.0000
3:123259520:GCAGA:G	acceptor_loss	1.0000
3:123259521:CAG:C	acceptor_gain	1.0000
3:123259521:CAGA:C	acceptor_loss	1.0000
3:123259522:A:AG	acceptor_gain	1.0000
3:123259522:A:G	acceptor_loss	1.0000
3:123259522:AGA:A	acceptor_gain	1.0000
3:123259522:AGAGT:A	acceptor_gain	1.0000
3:123259523:G:GA	acceptor_gain	1.0000

AlphaMissense

2011 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:123223645:T:C	L90P	0.999
3:123209270:T:A	L18H	0.998
3:123223632:T:C	F86L	0.998
3:123223634:C:A	F86L	0.998
3:123223634:C:G	F86L	0.998
3:123223656:T:C	F94L	0.998
3:123223657:T:C	F94S	0.998
3:123223658:C:A	F94L	0.998
3:123223658:C:G	F94L	0.998
3:123223719:T:C	F115L	0.998
3:123223721:T:A	F115L	0.998
3:123223721:T:G	F115L	0.998
3:123209243:T:A	V9D	0.997
3:123209264:T:C	L16P	0.997
3:123223581:A:C	S69R	0.997
3:123223583:C:A	S69R	0.997
3:123223583:C:G	S69R	0.997
3:123223626:T:C	F84L	0.997
3:123223628:C:A	F84L	0.997
3:123223628:C:G	F84L	0.997
3:123223636:T:C	L87P	0.997
3:123223633:T:C	F86S	0.996
3:123225125:G:C	K123N	0.996
3:123225125:G:T	K123N	0.996
3:123225132:T:G	Y126D	0.996
3:123209248:C:A	R11S	0.995
3:123209249:G:C	R11P	0.995
3:123209270:T:C	L18P	0.995
3:123245985:G:C	G210R	0.995
3:123223624:C:A	A83D	0.994

dbSNP variants (sampled 300 via entrez): RS1000079850 (3:123219489 A>G), RS1000109860 (3:123235473 C>G), RS1000131704 (3:123248321 A>G), RS1000167391 (3:123223278 C>T), RS1000212545 (3:123237272 A>G), RS1000255878 (3:123240834 C>T), RS1000280029 (3:123274502 A>G), RS1000306871 (3:123229494 CAAAGT>C), RS1000328377 (3:123261211 G>A), RS1000347648 (3:123234820 C>T), RS1000355543 (3:123228158 A>G), RS1000362726 (3:123242018 T>A,C,G), RS1000377389 (3:123273329 A>G), RS1000397332 (3:123248540 T>C), RS1000405058 (3:123216349 G>A)

Disease associations

OMIM: gene MIM:612442 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004899_9	Gestational age at birth (maternal effect)	4.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005112	gestational age
EFO:0005939	parental genotype effect measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases methylation	3
Valproic Acid	affects expression, decreases methylation, increases expression	3
Cisplatin	affects expression, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
trichostatin A	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Gallic Acid	increases expression	1
Hydrogen Peroxide	increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	decreases expression	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TK31	HAP1 SEC22A (-) 1	Cancer cell line	Male
CVCL_TK32	HAP1 SEC22A (-) 2	Cancer cell line	Male
CVCL_TK33	HAP1 SEC22A (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.