SCAMP1

gene
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Also known as SCAMP37

Summary

SCAMP1 (secretory carrier membrane protein 1, HGNC:10563) is a protein-coding gene on chromosome 5q14.1, encoding Secretory carrier-associated membrane protein 1 (O15126). Functions in post-Golgi recycling pathways.

This gene product belongs to the SCAMP family of proteins, which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that these protein family members may function at the same site during vesicular transport rather than in separate pathways. A pseudogene of this gene has been defined on chromosome 1. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 9522 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 25 total
  • MANE Select transcript: NM_004866

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10563
Approved symbolSCAMP1
Namesecretory carrier membrane protein 1
Location5q14.1
Locus typegene with protein product
StatusApproved
AliasesSCAMP37
Ensembl geneENSG00000085365
Ensembl biotypeprotein_coding
OMIM606911
Entrez9522

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000320280, ENST00000506858, ENST00000510030, ENST00000511551, ENST00000614488, ENST00000618166, ENST00000621999, ENST00000878187, ENST00000878188, ENST00000920041, ENST00000962697

RefSeq mRNA: 2 — MANE Select: NM_004866 NM_001290229, NM_004866

CCDS: CCDS75264, CCDS78025

Canonical transcript exons

ENST00000621999 — 9 exons

ExonStartEnd
ENSE000034670107842180178421960
ENSE000034780917841877578418903
ENSE000037166657844993378450034
ENSE000037242517841552078415618
ENSE000037296447847550478480739
ENSE000037326357836061778360728
ENSE000037380037841654178416649
ENSE000037420637838883778388914
ENSE000037506557845924578459362

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 98.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.2448 / max 385.2918, expressed in 1811 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
5720424.68801792
572005.67371618
572034.96741635
572054.17521505
572011.86651100
572021.4777948
571980.3090141
571990.087316

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pigmented layer of retinaUBERON:000178298.61gold quality
choroid plexus epitheliumUBERON:000391198.38gold quality
cortical plateUBERON:000534398.29gold quality
lateral nuclear group of thalamusUBERON:000273697.93gold quality
superior vestibular nucleusUBERON:000722797.86gold quality
Brodmann (1909) area 23UBERON:001355497.32gold quality
islet of LangerhansUBERON:000000697.24gold quality
secondary oocyteCL:000065597.23gold quality
buccal mucosa cellCL:000233697.21gold quality
cartilage tissueUBERON:000241897.08gold quality
medulla oblongataUBERON:000189696.92gold quality
seminal vesicleUBERON:000099896.86gold quality
Brodmann (1909) area 46UBERON:000648396.81gold quality
parietal lobeUBERON:000187296.62gold quality
middle temporal gyrusUBERON:000277196.50gold quality
endothelial cellCL:000011596.49gold quality
postcentral gyrusUBERON:000258196.46gold quality
trigeminal ganglionUBERON:000167596.40gold quality
ventral tegmental areaUBERON:000269196.40gold quality
superior frontal gyrusUBERON:000266196.37gold quality
ponsUBERON:000098896.33gold quality
entorhinal cortexUBERON:000272896.13gold quality
parotid glandUBERON:000183196.06gold quality
caput epididymisUBERON:000435895.98gold quality
mammalian vulvaUBERON:000099795.96gold quality
CA1 field of hippocampusUBERON:000388195.95gold quality
dorsal plus ventral thalamusUBERON:000189795.83gold quality
penisUBERON:000098995.82gold quality
oocyteCL:000002395.80gold quality
mucosa of paranasal sinusUBERON:000503095.80gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

248 targeting SCAMP1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4668-3P100.0068.742635
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-3163100.0077.238605
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-5692A100.0074.406850
HSA-MIR-8485100.0077.574731
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-453199.9969.703181
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-1213699.9872.815713
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-548N99.9871.944170
HSA-MIR-480399.9871.993117
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955

Literature-anchored findings (GeneRIF, showing 5)

  • RNA interference-mediated downregulation of SCAMP1 resulted in a marked reduction in cell migration and invasion, but not proliferation in tumor cell lines. (PMID:23653380)
  • SCAMP1 enhances Mtss1 anti-invasive function in HER2+/ER-/PR- breast cancer, by promoting its protein trafficking leading to elevated levels of RAC1-GTP and increased cell-cell adhesions. (PMID:29497041)
  • Prognostic role of SCAMP family in acute myeloid leukemia. (PMID:31988488)
  • Long Noncoding RNA SCAMP1 Targets miR-137/CXCL12 Axis to Boost Cell Invasion and Angiogenesis in Ovarian Cancer (PMID:32401536)
  • Multiomics Analysis of Endocytosis upon HBV Infection and Identification of SCAMP1 as a Novel Host Restriction Factor against HBV Replication. (PMID:35216324)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioscamp1ENSDARG00000036911
mus_musculusScamp1ENSMUSG00000021687
rattus_norvegicusScamp1ENSRNOG00000061582
drosophila_melanogasterScampFBGN0040285
caenorhabditis_elegansscm-1WBGENE00004743

Paralogs (4): SCAMP3 (ENSG00000116521), SCAMP2 (ENSG00000140497), SCAMP5 (ENSG00000198794), SCAMP4 (ENSG00000227500)

Protein

Protein identifiers

Secretory carrier-associated membrane protein 1O15126 (reviewed: O15126)

All UniProt accessions (5): O15126, A0A087WTX8, A0A087WU14, A0A087WXB0, A0A087WZA6

UniProt curated annotations — full annotation on UniProt →

Function. Functions in post-Golgi recycling pathways. Acts as a recycling carrier to the cell surface.

Subunit / interactions. Interacts with SYNRG and ITSN1. Interacts with SLC9A7.

Subcellular location. Golgi apparatus. trans-Golgi network membrane. Recycling endosome membrane.

Tissue specificity. Widely expressed, with highest expression in brain.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the SCAMP family.

Isoforms (2)

UniProt IDNamesCanonical?
O15126-11yes
O15126-22

RefSeq proteins (2): NP_001277158, NP_004857* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007273SCAMPFamily

Pfam: PF04144

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15126-F179.310.43

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, 2, 45

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation
R-HSA-168249Innate Immune System
R-HSA-168256Immune System

MSigDB gene sets: 334 (showing top): BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, FREAC2_01, REACTOME_INNATE_IMMUNE_SYSTEM, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, MORF_MSH3, GOCC_SECRETORY_GRANULE, MORF_BRCA1, MORF_ATRX, MITSIADES_RESPONSE_TO_APLIDIN_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, MORF_ESR1, NFKB_Q6, GOBP_EXOCYTOSIS

GO Biological Process (5): exocytosis (GO:0006887), post-Golgi vesicle-mediated transport (GO:0006892), endocytosis (GO:0006897), protein transport (GO:0015031), establishment of localization in cell (GO:0051649)

GO Molecular Function (2): protein domain specific binding (GO:0019904), protein binding (GO:0005515)

GO Cellular Component (13): trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), membrane (GO:0016020), clathrin-coated vesicle (GO:0030136), synaptic vesicle membrane (GO:0030672), trans-Golgi network membrane (GO:0032588), specific granule membrane (GO:0035579), zymogen granule membrane (GO:0042589), recycling endosome membrane (GO:0055038), endosome (GO:0005768), Golgi apparatus (GO:0005794), cytoplasmic vesicle membrane (GO:0030659), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Innate Immune System1
Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
vesicle-mediated transport2
secretory granule membrane2
endomembrane system2
cytoplasmic vesicle2
secretion by cell1
vesicle fusion to plasma membrane1
Golgi vesicle transport1
vesicle budding from membrane1
membrane invagination1
import into cell1
transport1
intracellular protein localization1
establishment of protein localization1
establishment of localization1
cellular localization1
protein binding1
binding1
Golgi apparatus subcompartment1
membrane1
cell periphery1
cellular anatomical structure1
coated vesicle1
synaptic vesicle1
exocytic vesicle membrane1
trans-Golgi network1
organelle membrane1
specific granule1
zymogen granule1
endosome membrane1
recycling endosome1
cytoplasm1
intracellular membrane-bounded organelle1
vesicle membrane1
cell junction1

Protein interactions and networks

STRING

1102 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCAMP1ITSN1Q15811773
SCAMP1SYNRGQ9UMZ2766
SCAMP1ITSN2Q9NZM3553
SCAMP1ARF6P26438502
SCAMP1EXOC5O00471479
SCAMP1RAB9AP51151460
SCAMP1STON2Q8WXE9445
SCAMP1HOOK3Q86VS8430
SCAMP1BAZ1AQ9NRL2429
SCAMP1LRRC8BQ6P9F7429
SCAMP1TBC1D15Q8TC07428
SCAMP1KIF5BP33176422
SCAMP1SLC44A1Q8WWI5420
SCAMP1RAB3BP20337418
SCAMP1HOOK1Q9UJC3415

IntAct

158 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
CD27TCAF2psi-mi:“MI:0914”(association)0.640
ENPP6SCAMP1psi-mi:“MI:0914”(association)0.640
ABCD4ABCD4psi-mi:“MI:0914”(association)0.640
LYPD3SCAMP1psi-mi:“MI:0914”(association)0.640
SCAMP1DNAJC13psi-mi:“MI:0915”(physical association)0.620
SCAMP1DNAJC13psi-mi:“MI:0914”(association)0.620
TASOR2SCAMP1psi-mi:“MI:0915”(physical association)0.560
ZMIZ2SCAMP1psi-mi:“MI:0915”(physical association)0.560
SCAMP1psi-mi:“MI:0915”(physical association)0.560
SCAMP1psi-mi:“MI:0915”(physical association)0.560
SCAMP1NDRG4psi-mi:“MI:0915”(physical association)0.560
SCAMP1PCYT1Apsi-mi:“MI:0915”(physical association)0.560
SCAMP1MTERF3psi-mi:“MI:0915”(physical association)0.560
SCAMP1THAP4psi-mi:“MI:0915”(physical association)0.560
SCAMP1PBX3psi-mi:“MI:0915”(physical association)0.560
SCAMP1SPG21psi-mi:“MI:0915”(physical association)0.560
SCAMP1ARFIP2psi-mi:“MI:0915”(physical association)0.560
SCAMP1ARFIP1psi-mi:“MI:0915”(physical association)0.560
SCAMP1PTPN9psi-mi:“MI:0915”(physical association)0.560

BioGRID (286): FAM208B (Two-hybrid), ZMIZ2 (Two-hybrid), KRTAP13-1 (Two-hybrid), SCAMP1 (Affinity Capture-RNA), SCAMP1 (Affinity Capture-RNA), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Affinity Capture-MS), SCAMP1 (Proximity Label-MS)

ESM2 similar proteins: A5D7K7, B4DJY2, D3Z1U7, D3ZWZ9, O09117, O15126, O15127, O46521, O62646, O77735, O89104, P13164, P13498, P17971, P52650, P56603, P59995, Q05B54, Q0VBF8, Q16563, Q28CV2, Q2MHH0, Q5TYP8, Q5VSE6, Q5VXT5, Q61462, Q62737, Q63881, Q66IQ1, Q69YW2, Q6DFT4, Q6GQE1, Q8BGA2, Q8BLV3, Q8C838, Q8HYZ1, Q8IXB3, Q8K021, Q91499, Q95L73

Diamond homologs: O14828, O15126, O15127, O35609, O77735, P56603, Q17QF8, Q28F21, Q58DF6, Q58DR5, Q5R5Z8, Q5RCY9, Q6GM42, Q6GPA8, Q6P0C7, Q8K021, Q8TAC9, Q969E2, Q9ERN0, Q9ET20, Q9JKD3, Q9JKE3, Q9JKV5, Q9LR68, Q0JAI9, Q6Z8F5, Q9SXA5, Q9SKT3, Q9M5P2, Q9C6X2, Q9ZTX0, Q60EA5, A2YMP7, Q75IC7, Q7F613, Q8H5X5

SIGNOR signaling

1 interactions.

AEffectBMechanism
EGFR“up-regulates activity”SCAMP1phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance10
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2015 predictions. Top by Δscore:

VariantEffectΔscore
5:78360726:AAGGT:Adonor_loss1.0000
5:78360730:T:Adonor_loss1.0000
5:78388830:A:AGacceptor_gain1.0000
5:78388834:TAG:Tacceptor_loss1.0000
5:78388835:A:AGacceptor_gain1.0000
5:78388835:A:Gacceptor_loss1.0000
5:78388835:AG:Aacceptor_gain1.0000
5:78388836:G:GTacceptor_gain1.0000
5:78388836:GG:Gacceptor_gain1.0000
5:78388910:GAACA:Gdonor_gain1.0000
5:78388913:CA:Cdonor_gain1.0000
5:78388915:G:GGdonor_gain1.0000
5:78415509:A:AGacceptor_gain1.0000
5:78415510:A:Gacceptor_gain1.0000
5:78415515:CCTA:Cacceptor_loss1.0000
5:78415516:CTA:Cacceptor_loss1.0000
5:78415518:A:AGacceptor_gain1.0000
5:78415518:AG:Aacceptor_loss1.0000
5:78415519:G:GTacceptor_gain1.0000
5:78415519:GC:Gacceptor_gain1.0000
5:78415519:GCC:Gacceptor_gain1.0000
5:78415519:GCCT:Gacceptor_gain1.0000
5:78415519:GCCTC:Gacceptor_gain1.0000
5:78415615:AAAG:Adonor_loss1.0000
5:78415618:GGTT:Gdonor_loss1.0000
5:78415619:G:Adonor_loss1.0000
5:78416536:TTTA:Tacceptor_loss1.0000
5:78416538:TAG:Tacceptor_loss1.0000
5:78416539:A:AGacceptor_gain1.0000
5:78416540:G:GGacceptor_gain1.0000

AlphaMissense

2245 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:78416587:T:CL94P1.000
5:78416598:G:CA98P1.000
5:78418789:T:AW120R1.000
5:78418789:T:CW120R1.000
5:78421932:T:AW202R1.000
5:78421932:T:CW202R1.000
5:78459249:T:AW247R1.000
5:78459249:T:CW247R1.000
5:78475520:G:CR290P1.000
5:78475547:C:AA299D1.000
5:78475559:T:CF303S1.000
5:78475589:T:AV313D1.000
5:78475600:G:CA317P1.000
5:78475601:C:AA317D1.000
5:78475613:C:AA321D1.000
5:78360696:T:CF9L0.999
5:78360697:T:GF9C0.999
5:78360698:T:AF9L0.999
5:78360698:T:GF9L0.999
5:78388897:T:CF40L0.999
5:78388898:T:GF40C0.999
5:78388899:C:AF40L0.999
5:78388899:C:GF40L0.999
5:78416575:G:CR90P0.999
5:78416578:A:CQ91P0.999
5:78416601:G:CA99P0.999
5:78416608:T:CL101S0.999
5:78416617:G:CR104P0.999
5:78418788:T:AN119K0.999
5:78418788:T:GN119K0.999

dbSNP variants (sampled 300 via entrez): RS1000034845 (5:78408667 C>G), RS1000062987 (5:78438087 A>G), RS1000076441 (5:78471750 A>G), RS1000083589 (5:78359737 G>C), RS1000098899 (5:78388358 T>C), RS1000131252 (5:78388138 C>T), RS1000135304 (5:78401222 T>C,G), RS1000176116 (5:78388443 C>G), RS1000183970 (5:78475334 A>G), RS1000245021 (5:78359640 C>G,T), RS1000249174 (5:78475927 G>A,T), RS1000293774 (5:78468623 T>C), RS1000300929 (5:78448992 C>T), RS1000319224 (5:78375614 T>C), RS1000329194 (5:78394828 G>A)

Disease associations

OMIM: gene MIM:606911 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST000461_21Hippocampal atrophy2.000000e-06
GCST003301_5Triglycerides7.000000e-08
GCST006412_23Intraocular pressure7.000000e-09
GCST90002400_689Plateletcrit2.000000e-12
GCST90002402_775Platelet count2.000000e-34

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0005039hippocampal atrophy
EFO:0004530triglyceride measurement
EFO:0004695intraocular pressure measurement
EFO:0007985platelet crit
EFO:0004309platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

56 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
cobaltous chlorideaffects cotreatment, increases expression3
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tetrachlorodibenzodioxinaffects expression, decreases expression2
Tretinoindecreases expression2
Valproic Acidincreases expression2
Cadmium Chloridedecreases reaction, increases abundance, increases palmitoylation, decreases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
testosterone enanthateaffects expression1
methylmercuric chloridedecreases expression1
uranyl acetateaffects expression1
pirinixic acidaffects binding, increases activity, increases expression1
lead acetateaffects cotreatment, decreases expression1
beta-lapachonedecreases expression1
zinc protoporphyrinaffects cotreatment, decreases expression1
sodium arsenitedecreases expression, increases abundance1
2-bromopalmitateincreases palmitoylation, decreases reaction, increases abundance1
lead chlorideaffects cotreatment, increases expression1
coumarindecreases phosphorylation1
cadmium sulfateaffects cotreatment, increases expression1
beta-methylcholineaffects expression1
tamibaroteneaffects expression1
di-n-butylphosphoric acidaffects expression1
indolo(3,2-b)carbazoledecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Rosiglitazoneincreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B2EMAbcam HeLa SCAMP1 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.