SMAP1

gene
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Also known as FLJ13159SMAP-1

Summary

SMAP1 (small ArfGAP 1, HGNC:19651) is a protein-coding gene on chromosome 6q13, encoding Stromal membrane-associated protein 1 (Q8IYB5). GTPase activating protein that acts on ARF6.

The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 60682 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 30 total — 1 pathogenic
  • MANE Select transcript: NM_001044305

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19651
Approved symbolSMAP1
Namesmall ArfGAP 1
Location6q13
Locus typegene with protein product
StatusApproved
AliasesFLJ13159, SMAP-1
Ensembl geneENSG00000112305
Ensembl biotypeprotein_coding
OMIM611372
Entrez60682

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 18 protein_coding

ENST00000316999, ENST00000370452, ENST00000370455, ENST00000439432, ENST00000445046, ENST00000619054, ENST00000894939, ENST00000894940, ENST00000894941, ENST00000894942, ENST00000939436, ENST00000939437, ENST00000960745, ENST00000960746, ENST00000960747, ENST00000960748, ENST00000960749, ENST00000960750

RefSeq mRNA: 4 — MANE Select: NM_001044305 NM_001044305, NM_001281439, NM_001281440, NM_021940

CCDS: CCDS43478, CCDS4973, CCDS64459, CCDS75478

Canonical transcript exons

ENST00000370455 — 11 exons

ExonStartEnd
ENSE000008103757077335070773425
ENSE000019457737086020070862003
ENSE000022283827079865770798737
ENSE000022338407085685970857030
ENSE000022800367083694170837028
ENSE000023051027085254070852664
ENSE000023101777085792270858229
ENSE000024733717075498070755065
ENSE000025027377073237870732511
ENSE000037895867079168970791769
ENSE000038940047066788370668141

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 97.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.5648 / max 157.9496, expressed in 1812 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
6847819.78791805
684767.17941736
684792.04131187
684771.1681807
684800.2274100
684750.160776

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534397.03gold quality
jejunal mucosaUBERON:000039996.38gold quality
mucosa of sigmoid colonUBERON:000499394.98gold quality
colonic mucosaUBERON:000031794.94gold quality
esophagus squamous epitheliumUBERON:000692094.63gold quality
epithelium of esophagusUBERON:000197694.45gold quality
oral cavityUBERON:000016794.17gold quality
ponsUBERON:000098893.88gold quality
jejunumUBERON:000211593.28gold quality
pharyngeal mucosaUBERON:000035592.89gold quality
duodenumUBERON:000211492.85gold quality
squamous epitheliumUBERON:000691492.55gold quality
skin of hipUBERON:000155492.44gold quality
upper leg skinUBERON:000426292.44gold quality
islet of LangerhansUBERON:000000692.01gold quality
ganglionic eminenceUBERON:000402391.87gold quality
superior vestibular nucleusUBERON:000722791.75gold quality
superior surface of tongueUBERON:000737191.72gold quality
sural nerveUBERON:001548891.54gold quality
rectumUBERON:000105291.28gold quality
penisUBERON:000098991.17gold quality
ileal mucosaUBERON:000033190.95gold quality
left testisUBERON:000453390.86gold quality
heart right ventricleUBERON:000208090.81gold quality
gastrocnemiusUBERON:000138890.79gold quality
gingivaUBERON:000182890.51gold quality
spermCL:000001990.48gold quality
muscle of legUBERON:000138390.45gold quality
pancreasUBERON:000126490.43gold quality
testisUBERON:000047390.39gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.72
E-MTAB-6386no220.66
E-CURD-112no2.42

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SMAD5

miRNA regulators (miRDB)

128 targeting SMAP1, 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-4262100.0073.263931
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-432-3P100.0067.86705
HSA-MIR-3163100.0077.238605
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-366299.9973.825684
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-607799.9968.042299
HSA-MIR-428299.9975.366408
HSA-MIR-223-3P99.9970.141140
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-477599.9875.006394
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-806899.9873.852376
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-590-3P99.9674.346478
HSA-MIR-493-5P99.9672.472382
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-767-5P99.9570.85993
HSA-MIR-101-3P99.9475.032230
HSA-MIR-22-3P99.9368.13917

Literature-anchored findings (GeneRIF, showing 5)

  • SMAP1 may be an ADP-ribosylation factor 6 (Arf6)GAP that specifically regulates one of the multiple functions of Arf6, namely, clathrin-dependent endocytosis (PMID:15659652)
  • SMAP1 loss-of-function mutations in microsatellite instability colorectal cancer may contribute to the emerging oncogenic pathway involving abnormal Arf6 regulation. (PMID:23752192)
  • Results also demonstrated a physical association between SMAP1 and SMAP2, which might serve as a basis for a functional interaction, and identified the intramolecular domains responsible for this association (PMID:25281535)
  • The study identified a region on chromosome 6 comprising the genes SMAP1, B3GAT2, and RIMS1 as novel susceptibility locus for pediatric venous thromboembolism. (PMID:28011674)
  • Pals1 functions in redundancy with SMAP1 to inhibit Arf6 in order to prevent Rac1-dependent colorectal cancer cell migration and invasion. (PMID:36494580)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosmap1ENSDARG00000031302
mus_musculusSmap1ENSMUSG00000026155
rattus_norvegicusSmap1ENSRNOG00000049127

Paralogs (28): ARAP2 (ENSG00000047365), ACAP1 (ENSG00000072818), SMAP2 (ENSG00000084070), ASAP3 (ENSG00000088280), ARFGAP1 (ENSG00000101199), ADAP1 (ENSG00000105963), AGFG2 (ENSG00000106351), GIT1 (ENSG00000108262), ACAP2 (ENSG00000114331), ARAP3 (ENSG00000120318), ACAP3 (ENSG00000131584), AGAP3 (ENSG00000133612), AGAP2 (ENSG00000135439), APPL2 (ENSG00000136044), GIT2 (ENSG00000139436), ARFGAP2 (ENSG00000149182), ASAP2 (ENSG00000151693), ASAP1 (ENSG00000153317), APPL1 (ENSG00000157500), AGAP1 (ENSG00000157985), AGAP5 (ENSG00000172650), AGFG1 (ENSG00000173744), ADAP2 (ENSG00000184060), ARAP1 (ENSG00000186635), AGAP4 (ENSG00000188234), AGAP6 (ENSG00000204149), AGAP9 (ENSG00000204172), ARFGAP3 (ENSG00000242247)

Protein

Protein identifiers

Stromal membrane-associated protein 1Q8IYB5 (reviewed: Q8IYB5)

All UniProt accessions (4): A0A087X1X9, Q8IYB5, H0Y5G0, Q5T6I8

UniProt curated annotations — full annotation on UniProt →

Function. GTPase activating protein that acts on ARF6. Plays a role in clathrin-dependent endocytosis. May play a role in erythropoiesis.

Subunit / interactions. Interacts with ARF6. Interacts with clathrin heavy chains via the clathrin box-like motif.

Subcellular location. Cell membrane.

Tissue specificity. Detected in bone marrow, adrenal gland, trachea, lymph node, spinal cord, peripheral blood leukocytes, thyroid and stomach.

Isoforms (3)

UniProt IDNamesCanonical?
Q8IYB5-11, SMAP1Ayes
Q8IYB5-22, SMAP1B
Q8IYB5-33

RefSeq proteins (4): NP_001037770, NP_001268368, NP_001268369, NP_068759 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001164ArfGAP_domDomain
IPR037278ARFGAP/RecOHomologous_superfamily
IPR038508ArfGAP_dom_sfHomologous_superfamily
IPR044732ArfGAP_SMAP1-likeDomain
IPR051718ARF_GTPase-activatingFamily

Pfam: PF01412

UniProt features (29 total): helix 8, compositionally biased region 5, turn 3, strand 3, splice variant 2, region of interest 2, chain 1, domain 1, sequence variant 1, sequence conflict 1, zinc finger region 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2CRRSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IYB5-F162.060.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 190 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_ERYTHROCYTE_DIFFERENTIATION, GOBP_MYELOID_CELL_HOMEOSTASIS, ATACCTC_MIR202, GOBP_ERYTHROCYTE_HOMEOSTASIS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_HEMOPOIESIS, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, ACATTCC_MIR1_MIR206, GOBP_POSITIVE_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_ERYTHROCYTE_DIFFERENTIATION

GO Biological Process (2): positive regulation of erythrocyte differentiation (GO:0045648), regulation of clathrin-dependent endocytosis (GO:2000369)

GO Molecular Function (5): GTPase activator activity (GO:0005096), zinc ion binding (GO:0008270), clathrin binding (GO:0030276), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
erythrocyte differentiation1
positive regulation of myeloid cell differentiation1
regulation of erythrocyte differentiation1
regulation of receptor-mediated endocytosis1
clathrin-dependent endocytosis1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
transition metal ion binding1
protein binding1
binding1
cation binding1
intracellular anatomical structure1
membrane1
cell periphery1

Protein interactions and networks

STRING

736 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SMAP1MAP1BP46821671
SMAP1ARF6P26438644
SMAP1CLTCQ00610563
SMAP1DENND5BQ6ZUT9521
SMAP1LGSNQ5TDP6507
SMAP1CLSTN1O94985498
SMAP1RASA1P20936481
SMAP1LYG1Q8N1E2478
SMAP1TBCDQ9BTW9473
SMAP1TFRCP02786470
SMAP1RBP2P50120449
SMAP1ZSWIM3Q96MP5447
SMAP1IFT70AQ86WT1434
SMAP1EPM2AIP1Q7L775419
SMAP1OR4Q3Q8NH05410

IntAct

29 interactions, top by confidence:

ABTypeScore
CNOT3CNOT1psi-mi:“MI:0914”(association)0.740
BAG2HGSpsi-mi:“MI:0914”(association)0.530
ZNF829TRIM28psi-mi:“MI:0914”(association)0.530
GPS1PXDNLpsi-mi:“MI:0914”(association)0.530
HSPA2DNAJC13psi-mi:“MI:0914”(association)0.530
OIP5CYTH3psi-mi:“MI:0914”(association)0.530
ENGSMAP1psi-mi:“MI:0407”(direct interaction)0.440
SMAP1NPWpsi-mi:“MI:0915”(physical association)0.400
JUNTPM3psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
SLC16A11ESYT2psi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
hspa1a_hspa1b_human-1SHTN1psi-mi:“MI:0914”(association)0.350
MICU2ACOX3psi-mi:“MI:0914”(association)0.350
B3GALT2LIG1psi-mi:“MI:0914”(association)0.350
DDX28UBA6psi-mi:“MI:0914”(association)0.350
HSPA8PLEKHG3psi-mi:“MI:0914”(association)0.350
MMP14BIN1psi-mi:“MI:0914”(association)0.350
MRPL49UBA6psi-mi:“MI:0914”(association)0.350
LRRK2SF3B1psi-mi:“MI:0914”(association)0.350
ALKNUDT19psi-mi:“MI:2364”(proximity)0.270
EGFRFAM171A2psi-mi:“MI:2364”(proximity)0.270
FGFR1BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
FGFR4SH3PXD2Bpsi-mi:“MI:2364”(proximity)0.270
ROR2SH3PXD2Bpsi-mi:“MI:2364”(proximity)0.270

BioGRID (76): SMAP1 (Affinity Capture-MS), HSPA1L (Affinity Capture-MS), KLHL18 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), KLHL18 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), SMAP1 (Affinity Capture-MS), ARF6 (Biochemical Activity), CLTC (Reconstituted Complex)

ESM2 similar proteins: A0JMZ1, A1L209, A1L2F3, A1L3I5, A2AWT3, A4FUE7, A6QQM4, O82171, O94519, P97868, Q08AZ1, Q14CW9, Q1W1G1, Q22122, Q2HJG4, Q2YDJ0, Q32KN7, Q5EAW4, Q5PPV5, Q5REC0, Q5TFG8, Q5ZMS6, Q618K0, Q62920, Q64GL0, Q66HC1, Q6DGN6, Q6NRP6, Q6P1U3, Q6V5K9, Q7SXT7, Q7Z6E9, Q801E2, Q8BJH1, Q8CI51, Q8H100, Q8IMP6, Q8IYB5, Q8R550, Q91W18

Diamond homologs: A1L520, A1Z7A6, A5PK26, A6NIR3, O43150, O74345, O75689, O80925, O82171, O94601, O97902, P35197, P38682, P40529, P52594, Q04412, Q09531, Q0WQQ1, Q10165, Q10367, Q14161, Q15027, Q15057, Q17R07, Q1AAU6, Q1ZXH8, Q28CM8, Q2TA45, Q3MID3, Q3UHD9, Q4KLH5, Q4KLN7, Q4LDD4, Q4R4C9, Q5F413, Q5FVC7, Q5R787, Q5RAT7, Q5U464, Q5VTM2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance25
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4278487NM_001044305.3(SMAP1):c.577-1G>TPathogenic

SpliceAI

3985 predictions. Top by Δscore:

VariantEffectΔscore
6:70670053:G:GTdonor_gain1.0000
6:70732357:T:TAacceptor_gain1.0000
6:70732371:A:AGacceptor_gain1.0000
6:70732375:TAG:Tacceptor_loss1.0000
6:70732376:A:ATacceptor_loss1.0000
6:70732377:G:Aacceptor_loss1.0000
6:70732507:TACAG:Tdonor_loss1.0000
6:70732508:ACAG:Adonor_loss1.0000
6:70732509:CAG:Cdonor_loss1.0000
6:70732510:AGG:Adonor_loss1.0000
6:70732511:GGTAA:Gdonor_loss1.0000
6:70732512:G:Tdonor_loss1.0000
6:70732513:T:Gdonor_loss1.0000
6:70754975:TATA:Tacceptor_loss1.0000
6:70754977:TAGT:Tacceptor_loss1.0000
6:70754978:A:AGacceptor_gain1.0000
6:70754978:AGT:Aacceptor_gain1.0000
6:70754978:AGTG:Aacceptor_loss1.0000
6:70754979:G:GTacceptor_gain1.0000
6:70754979:GT:Gacceptor_gain1.0000
6:70754979:GTG:Gacceptor_gain1.0000
6:70754979:GTGC:Gacceptor_gain1.0000
6:70754979:GTGCA:Gacceptor_gain1.0000
6:70755061:GATCA:Gdonor_gain1.0000
6:70755062:A:Gdonor_gain1.0000
6:70755066:G:GGdonor_gain1.0000
6:70830704:G:GTdonor_gain1.0000
6:70836938:A:Gacceptor_gain1.0000
6:70836939:A:ATacceptor_loss1.0000
6:70836939:A:Gacceptor_gain1.0000

AlphaMissense

3066 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:70668085:T:AL21Q1.000
6:70668085:T:CL21P1.000
6:70668094:T:CL24P1.000
6:70668097:T:CL25P1.000
6:70668113:C:AN30K1.000
6:70668113:C:GN30K1.000
6:70668120:T:AC33S1.000
6:70668120:T:CC33R1.000
6:70668120:T:GC33G1.000
6:70668121:G:AC33Y1.000
6:70668121:G:CC33S1.000
6:70668121:G:TC33F1.000
6:70668122:C:GC33W1.000
6:70668124:C:AA34D1.000
6:70668126:G:CD35H1.000
6:70668126:G:TD35Y1.000
6:70668129:T:AC36S1.000
6:70668129:T:CC36R1.000
6:70668130:G:AC36Y1.000
6:70668130:G:CC36S1.000
6:70668130:G:TC36F1.000
6:70668131:C:GC36W1.000
6:70668135:G:CA38P1.000
6:70732380:C:TP41S1.000
6:70732381:C:AP41H1.000
6:70732381:C:GP41R1.000
6:70732384:G:CR42P1.000
6:70732386:T:AW43R1.000
6:70732386:T:CW43R1.000
6:70732386:T:GW43G1.000

dbSNP variants (sampled 300 via entrez): RS1000004784 (6:70722014 T>C), RS1000015608 (6:70787051 A>G), RS1000021285 (6:70754876 TAATA>T), RS1000024910 (6:70778394 T>C), RS1000025287 (6:70819231 T>G), RS1000039322 (6:70674195 C>T), RS1000042444 (6:70744017 T>A), RS1000047296 (6:70851004 G>A,T), RS1000054277 (6:70734399 G>T), RS1000070890 (6:70728141 A>G), RS1000074824 (6:70765671 G>A), RS1000107162 (6:70686662 A>G), RS1000109817 (6:70667966 C>A,T), RS1000150335 (6:70674244 C>A), RS1000156781 (6:70825876 C>T)

Disease associations

OMIM: gene MIM:611372 | disease phenotypes: MIM:617391

GenCC curated gene-disease

Mondo (1): developmental and epileptic encephalopathy, 54 (MONDO:0033363)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003518_15Daytime sleep phenotypes4.000000e-06
GCST009193_5Pars opercularis volume3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007828daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression3
cobaltous chlorideincreases expression2
Valproic Acidaffects expression, decreases expression, increases methylation2
Cadmium Chloridedecreases expression, increases expression2
aristolochic acid Idecreases expression1
chloroacetaldehydeaffects expression1
triphenyl phosphateaffects expression1
uranyl acetateaffects expression1
sodium arseniteincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
adefovir dipivoxildecreases expression1
ICG 001decreases expression1
jinfukangaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Cidofovirdecreases expression1
Air Pollutantsincreases abundance, decreases expression1
Ethanolincreases expression1
Benzo(a)pyreneincreases methylation1
Carbamazepineaffects expression1
Carcinogensdecreases expression1
Cisplatinaffects cotreatment, decreases expression1
Clodronic Acidincreases expression1
Dieldrinincreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Mutagensdecreases expression1
Oxygenincreases expression1

Clinical trials (associated diseases)

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