SCAMP4

Summary

SCAMP4 (secretory carrier membrane protein 4, HGNC:30385) is a protein-coding gene on chromosome 19p13.3, encoding Secretory carrier-associated membrane protein 4 (Q969E2). Probably involved in membrane protein trafficking.

Secretory carrier membrane proteins (SCAMPs) are widely distributed integral membrane proteins implicated in membrane trafficking. Most SCAMPs (e.g., SCAMP1; MIM 606911) have N-terminal cytoplasmic NPF (arg-pro-phe) repeats, 4 central transmembrane regions, and a short C-terminal cytoplasmic tail. These SCAMPs likely have a role in endocytosis that is mediated by their NPF repeats. Other SCAMPs, such as SCAMP4, lack the NPF repeats and are therefore unlikely to function in endocytosis (summary by Fernandez-Chacon and Sudhof, 2000 [PubMed 11050114]).

Source: NCBI Gene 113178 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 86 total
• MANE Select transcript: NM_079834

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30385
Approved symbol	SCAMP4
Name	secretory carrier membrane protein 4
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33847
Ensembl gene	ENSG00000227500
Ensembl biotype	protein_coding
OMIM	613764
Entrez	113178

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 9 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000316097, ENST00000409472, ENST00000411971, ENST00000414057, ENST00000452128, ENST00000460767, ENST00000472442, ENST00000489554, ENST00000585335, ENST00000588555, ENST00000588907, ENST00000590266, ENST00000621748, ENST00000873398, ENST00000922201

RefSeq mRNA: 3 — MANE Select: NM_079834 NM_001329539, NM_001329540, NM_079834

CCDS: CCDS45903, CCDS86689

Canonical transcript exons

ENST00000316097 — 7 exons

Exon	Start	End
ENSE00001576841	1924108	1926013
ENSE00001938986	1905399	1905439
ENSE00003526486	1917694	1917822
ENSE00003544220	1914979	1915026
ENSE00003565549	1918889	1918990
ENSE00003666979	1918127	1918283
ENSE00003746686	1923070	1923187

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 98.17.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9374 / max 54.2742, expressed in 598 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173012	47.5812	1820
173017	0.8409	533
173016	0.0631	34
173011	0.0334	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	98.17	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	95.73	gold quality
right lobe of thyroid gland	UBERON:0001119	95.54	gold quality
left lobe of thyroid gland	UBERON:0001120	94.84	gold quality
lower esophagus mucosa	UBERON:0035834	94.55	gold quality
stromal cell of endometrium	CL:0002255	94.47	gold quality
spinal cord	UBERON:0002240	94.39	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.02	gold quality
metanephros cortex	UBERON:0010533	94.02	gold quality
minor salivary gland	UBERON:0001830	93.95	gold quality
thyroid gland	UBERON:0002046	93.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.50	gold quality
body of pancreas	UBERON:0001150	93.45	gold quality
adenohypophysis	UBERON:0002196	93.40	gold quality
endocervix	UBERON:0000458	93.12	gold quality
left uterine tube	UBERON:0001303	93.05	gold quality
cerebellar hemisphere	UBERON:0002245	93.01	gold quality
cerebellar cortex	UBERON:0002129	92.87	gold quality
right ovary	UBERON:0002118	92.68	gold quality
left ovary	UBERON:0002119	92.53	gold quality
body of stomach	UBERON:0001161	92.41	gold quality
gall bladder	UBERON:0002110	92.29	gold quality
mucosa of transverse colon	UBERON:0004991	92.24	gold quality
skin of abdomen	UBERON:0001416	92.15	gold quality
pituitary gland	UBERON:0000007	92.10	gold quality
esophagus mucosa	UBERON:0002469	92.06	gold quality
skin of leg	UBERON:0001511	92.04	gold quality
transverse colon	UBERON:0001157	91.90	gold quality
upper lobe of left lung	UBERON:0008952	91.88	gold quality
ectocervix	UBERON:0012249	91.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

81 targeting SCAMP4, 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-6870-5P	99.99	68.55	2115
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-6132	99.60	65.83	1554

Literature-anchored findings (GeneRIF, showing 1)

• secretory carrier membrane protein 4 (SCAMP4) levels were strikingly elevated on the surface of senescent cells compared with proliferating cells (PMID:29967290)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	scamp4	ENSDARG00000010531
mus_musculus	Scamp4	ENSMUSG00000113949
rattus_norvegicus	Scamp4	ENSRNOG00000018271
drosophila_melanogaster	Scamp	FBGN0040285
caenorhabditis_elegans	scm-1	WBGENE00004743

Paralogs (4): SCAMP1 (ENSG00000085365), SCAMP3 (ENSG00000116521), SCAMP2 (ENSG00000140497), SCAMP5 (ENSG00000198794)

Protein

Protein identifiers

Secretory carrier-associated membrane protein 4 — Q969E2 (reviewed: Q969E2)

All UniProt accessions (6): Q969E2, A0A087WU01, A0A087WVT5, A0A087WYP4, C9JWM2, K7EJJ4

UniProt curated annotations — full annotation on UniProt →

Function. Probably involved in membrane protein trafficking.

Subcellular location. Membrane.

Similarity. Belongs to the SCAMP family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q969E2-1	1	yes
Q969E2-2	2
Q969E2-3	3

RefSeq proteins (3): NP_001316468, NP_001316469, NP_524558* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007273	SCAMP	Family

Pfam: PF04144

UniProt features (12 total): transmembrane region 4, topological domain 2, splice variant 2, chain 1, sequence variant 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969E2-F1	86.24	0.62

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 (1): 194

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, GOCC_TRANS_GOLGI_NETWORK, ONKEN_UVEAL_MELANOMA_UP, GROSS_HYPOXIA_VIA_HIF1A_UP, GOBP_SECRETION, CYTAGCAAY_UNKNOWN, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, TCCCRNNRTGC_UNKNOWN, LIU_SOX4_TARGETS_DN, SANSOM_APC_MYC_TARGETS, GOCC_RECYCLING_ENDOSOME_MEMBRANE, chr19p13

GO Biological Process (2): exocytosis (GO:0006887), protein transport (GO:0015031)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): trans-Golgi network membrane (GO:0032588), recycling endosome membrane (GO:0055038), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vesicle-mediated transport	1
secretion by cell	1
vesicle fusion to plasma membrane	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
binding	1
trans-Golgi network	1
organelle membrane	1
endosome membrane	1
recycling endosome	1
cellular anatomical structure	1

Protein interactions and networks

STRING

588 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCAMP4	FAM174B	Q3ZCQ3	477
SCAMP4	XXYLT1	Q8NBI6	460
SCAMP4	DUS3L	Q96G46	408
SCAMP4	REXO1	Q8N1G1	401
SCAMP4	ADAT3	Q96EY9	390
SCAMP4	SH3GL1	Q99961	363
SCAMP4	NIPSNAP3A	Q9UFN0	337
SCAMP4	NMRK2	Q9NPI5	327
SCAMP4	ABHD17A	Q96GS6	311
SCAMP4	ZNF460	Q14592	307
SCAMP4	RNF44	Q7L0R7	302
SCAMP4	ITPRIPL1	Q6GPH6	302
SCAMP4	NAA50	Q9GZZ1	292
SCAMP4	SYPL1	Q16563	286
SCAMP4	KLHL15	Q96M94	286

IntAct

81 interactions, top by confidence:

A	B	Type	Score
SCAMP4	CGRRF1	psi-mi:“MI:0915”(physical association)	0.560
SCAMP4	MDFI	psi-mi:“MI:0915”(physical association)	0.560
BIK	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
SCAMP4	SPAG4	psi-mi:“MI:0915”(physical association)	0.560
GPR152	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
SCAMP4	TMEM147	psi-mi:“MI:0915”(physical association)	0.560
KCNJ6	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
SLC10A1	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
EBP	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
EVI2B	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
CLDN7	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
SLC10A6	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
AQP6	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
SCAMP4	ABHD6	psi-mi:“MI:0915”(physical association)	0.560
GPR37	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
GRN	SCAMP4	psi-mi:“MI:0915”(physical association)	0.560
SCAMP4	GRN	psi-mi:“MI:0915”(physical association)	0.560
SCAMP4	WFS1	psi-mi:“MI:0915”(physical association)	0.560
GDPD5	GOLIM4	psi-mi:“MI:0914”(association)	0.530
REEP5	SCAMP1	psi-mi:“MI:0914”(association)	0.530

BioGRID (47): SCAMP4 (Proximity Label-MS), SCAMP4 (Two-hybrid), SCAMP4 (Affinity Capture-MS), SCAMP4 (Affinity Capture-MS), SCAMP4 (Affinity Capture-MS), SCAMP4 (Affinity Capture-RNA), SCAMP4 (Affinity Capture-MS), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid), SCAMP4 (Two-hybrid)

ESM2 similar proteins: A1CKG4, A1D708, A2XSY1, A4R2N5, A6QRX6, A6RRF7, A7EMV1, B0XXU1, B2AR67, D4A9I3, O46521, O95214, O95807, P13498, P52650, Q0CNZ5, Q0JDK9, Q0V0G4, Q17QF8, Q1E1E0, Q28F21, Q2GSS4, Q32PD8, Q3ZC23, Q4WXT2, Q58DF6, Q5R5Z8, Q5RCY9, Q5RDE9, Q61462, Q62737, Q6CC06, Q6GM42, Q6GPA8, Q6P0C7, Q6PDU4, Q7S693, Q8BG21, Q8K3C0, Q8LEK2

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

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1936 predictions. Top by Δscore:

Variant	Effect	Δscore
19:1905437:CAGG:C	donor_loss	1.0000
19:1905438:AGG:A	donor_loss	1.0000
19:1905438:AGGT:A	donor_loss	1.0000
19:1905440:G:GA	donor_loss	1.0000
19:1914974:TCCA:T	acceptor_loss	1.0000
19:1914977:A:AC	acceptor_loss	1.0000
19:1914977:AGGC:A	acceptor_gain	1.0000
19:1914978:GGCG:G	acceptor_gain	1.0000
19:1915027:G:GA	donor_loss	1.0000
19:1915028:T:A	donor_loss	1.0000
19:1917683:T:TA	acceptor_gain	1.0000
19:1917689:TACA:T	acceptor_loss	1.0000
19:1917690:ACAG:A	acceptor_loss	1.0000
19:1917691:C:G	acceptor_gain	1.0000
19:1917691:CA:C	acceptor_loss	1.0000
19:1917692:A:AG	acceptor_gain	1.0000
19:1917692:AGA:A	acceptor_loss	1.0000
19:1917693:G:GC	acceptor_gain	1.0000
19:1917693:GA:G	acceptor_gain	1.0000
19:1917693:GAA:G	acceptor_gain	1.0000
19:1917693:GAAA:G	acceptor_gain	1.0000
19:1917693:GAAAA:G	acceptor_gain	1.0000
19:1917818:G:GT	donor_gain	1.0000
19:1917818:GATGT:G	donor_gain	1.0000
19:1917819:ATGT:A	donor_gain	1.0000
19:1917820:TGTGT:T	donor_loss	1.0000
19:1917821:GT:G	donor_gain	1.0000
19:1917821:GTGTG:G	donor_loss	1.0000
19:1917823:G:GG	donor_gain	1.0000
19:1917823:GT:G	donor_loss	1.0000

AlphaMissense

1502 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:1917708:T:C	F8L	0.997
19:1917710:C:A	F8L	0.997
19:1917710:C:G	F8L	0.997
19:1918152:C:A	N54K	0.997
19:1918152:C:G	N54K	0.997
19:1923074:T:A	W134R	0.996
19:1923074:T:C	W134R	0.996
19:1918917:T:C	F108L	0.995
19:1918919:T:A	F108L	0.995
19:1918919:T:G	F108L	0.995
19:1917816:T:A	W44R	0.993
19:1917816:T:C	W44R	0.993
19:1918908:T:C	F105L	0.993
19:1918910:C:A	F105L	0.993
19:1918910:C:G	F105L	0.993
19:1918240:T:C	C84R	0.992
19:1918255:T:A	W89R	0.992
19:1918255:T:C	W89R	0.992
19:1923072:G:A	G133D	0.992
19:1918164:C:G	C58W	0.990
19:1918252:T:C	C88R	0.990
19:1918983:G:C	G130R	0.990
19:1917707:C:A	N7K	0.989
19:1917707:C:G	N7K	0.989
19:1918283:G:C	R98P	0.989
19:1923158:G:C	A162P	0.989
19:1917772:T:C	I29T	0.988
19:1923146:T:C	F158L	0.988
19:1923148:C:A	F158L	0.988
19:1923148:C:G	F158L	0.988

dbSNP variants (sampled 300 via entrez): RS1000061983 (19:1905920 A>G), RS1000068178 (19:1923491 G>T), RS1000075930 (19:1925425 C>T), RS1000338738 (19:1916785 C>T), RS1000350701 (19:1919254 A>C,G), RS1000465288 (19:1919432 A>G), RS1000485286 (19:1912694 T>C,G), RS1000547425 (19:1911345 G>T), RS1000586513 (19:1925913 C>CT), RS1000664280 (19:1905257 G>A,T), RS1000665052 (19:1911552 G>A,T), RS1000693388 (19:1922915 G>A,C), RS1000936601 (19:1915370 T>C), RS1000964022 (19:1924681 G>A,C), RS1001080241 (19:1924745 G>A)

Disease associations

OMIM: gene MIM:613764 | disease phenotypes: MIM:615286

GenCC curated gene-disease

Mondo (1): intellectual disability-strabismus syndrome (MONDO:0014119)

Orphanet (1): Intellectual disability-strabismus syndrome (Orphanet:363528)

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol F	increases expression, affects cotreatment	2
sodium arsenite	increases abundance, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
titanium dioxide	increases expression	1
beta-lapachone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol AF	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	increases expression	1
Fulvestrant	increases methylation	1
Air Pollutants	increases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Azacitidine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	increases phosphorylation	1
Cisplatin	affects expression	1
Dexamethasone	affects cotreatment, increases expression	1
Bucladesine	increases expression, affects cotreatment	1
Estradiol	affects cotreatment, increases expression	1
Etoposide	affects expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Medroxyprogesterone Acetate	affects cotreatment, increases expression	1
Gold Compounds	increases expression	1

Clinical trials (associated diseases)

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