STAC

gene
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Also known as STAC1

Summary

STAC (SH3 and cysteine rich domain, HGNC:11353) is a protein-coding gene on chromosome 3p22.3-p22.2, encoding SH3 and cysteine-rich domain-containing protein (Q99469). Promotes expression of the ion channel CACNA1H at the cell membrane, and thereby contributes to the regulation of channel activity.

Predicted to enable transmembrane transporter binding activity. Predicted to be involved in positive regulation of protein localization to plasma membrane; positive regulation of voltage-gated calcium channel activity; and skeletal muscle contraction. Predicted to act upstream of or within cellular response to heat; muscle contraction; and regulation of voltage-gated calcium channel activity. Predicted to be located in cytoplasmic side of plasma membrane.

Source: NCBI Gene 6769 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 63 total
  • MANE Select transcript: NM_003149

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11353
Approved symbolSTAC
NameSH3 and cysteine rich domain
Location3p22.3-p22.2
Locus typegene with protein product
StatusApproved
AliasesSTAC1
Ensembl geneENSG00000144681
Ensembl biotypeprotein_coding
OMIM602317
Entrez6769

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000273183, ENST00000427486, ENST00000434649, ENST00000457375, ENST00000465064, ENST00000473452, ENST00000476388, ENST00000486143, ENST00000903141, ENST00000903142, ENST00000903143, ENST00000929285

RefSeq mRNA: 2 — MANE Select: NM_003149 NM_001292049, NM_003149

CCDS: CCDS2662, CCDS77722

Canonical transcript exons

ENST00000273183 — 11 exons

ExonStartEnd
ENSE000009664673650574636505834
ENSE000009664693652884836528985
ENSE000011507373654619136548007
ENSE000018343043638050436380754
ENSE000035117883649315136493229
ENSE000035148933648299236483092
ENSE000035260443644336436443640
ENSE000035589023648497736485058
ENSE000036646933648613436486249
ENSE000036760183650439336504457
ENSE000037846723652869636528747

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 92.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.2467 / max 183.1831, expressed in 1033 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
360342.1117729
360311.6277760
360330.4111223
360320.096231

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
dorsal root ganglionUBERON:000004492.25gold quality
periodontal ligamentUBERON:000826687.75gold quality
trigeminal ganglionUBERON:000167584.18gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.96gold quality
diaphragmUBERON:000110383.77gold quality
ascending aortaUBERON:000149683.42gold quality
thoracic aortaUBERON:000151583.21gold quality
calcaneal tendonUBERON:000370181.06gold quality
descending thoracic aortaUBERON:000234580.28gold quality
aortaUBERON:000094778.18gold quality
olfactory bulbUBERON:000226477.81gold quality
pancreatic ductal cellCL:000207977.69silver quality
type B pancreatic cellCL:000016977.35gold quality
cerebellar cortexUBERON:000212976.18gold quality
cerebellar hemisphereUBERON:000224576.16gold quality
epithelial cell of pancreasCL:000008375.49silver quality
cerebellumUBERON:000203775.36gold quality
right hemisphere of cerebellumUBERON:001489074.99gold quality
visceral pleuraUBERON:000240174.97gold quality
mucosa of urinary bladderUBERON:000125974.86gold quality
popliteal arteryUBERON:000225074.45gold quality
tibial arteryUBERON:000761074.42gold quality
prostate glandUBERON:000236774.26gold quality
ventricular zoneUBERON:000305374.22gold quality
right lungUBERON:000216773.47gold quality
lungUBERON:000204873.27gold quality
smooth muscle tissueUBERON:000113573.11gold quality
upper lobe of left lungUBERON:000895273.08gold quality
ganglionic eminenceUBERON:000402372.89gold quality
upper lobe of lungUBERON:000894872.87gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-7008yes46.86
E-ANND-3no4.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

96 targeting STAC, 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-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-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-3646100.0073.565283
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-366299.9973.825684
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-391099.9571.132227
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-430299.8967.941187
HSA-MIR-605-3P99.8869.221833
HSA-MIR-137-3P99.8774.742401
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-449299.8768.253611
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351

Literature-anchored findings (GeneRIF, showing 2)

  • our data establish Stac1 as an important modulator of T-type channel expression and provide new insights into the molecular mechanisms underlying the trafficking of T-type channels to the plasma membrane. (PMID:27149520)
  • Our findings suggest that a variant upstream of STAC1 is associated with placebo response, which might have implications for treatment optimization, clinical trial design and drug development. (PMID:28696415)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriostacENSDARG00000074004
mus_musculusStacENSMUSG00000032502
rattus_norvegicusStacENSRNOG00000008865

Paralogs (2): STAC2 (ENSG00000141750), STAC3 (ENSG00000185482)

Protein

Protein identifiers

SH3 and cysteine-rich domain-containing proteinQ99469 (reviewed: Q99469)

Alternative names: Src homology 3 and cysteine-rich domain-containing protein

All UniProt accessions (4): Q99469, C9J3Z9, E9PEA7, F8WB25

UniProt curated annotations — full annotation on UniProt →

Function. Promotes expression of the ion channel CACNA1H at the cell membrane, and thereby contributes to the regulation of channel activity. Plays a minor and redundant role in promoting the expression of calcium channel CACNA1S at the cell membrane, and thereby contributes to increased channel activity. Slows down the inactivation rate of the calcium channel CACNA1C.

Subunit / interactions. Interacts (via SH3 domains) with CACNA1S. Interacts with CACNA1H. Interacts with CACNA1C.

Subcellular location. Cytoplasm. Cytosol. Cell membrane. Sarcolemma.

RefSeq proteins (2): NP_001278978, NP_003140* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001452SH3_domainDomain
IPR002219PKC_DAG/PEDomain
IPR035508STAC1_SH3Domain
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR039688STAC1/2/3Family
IPR046349C1-like_sfHomologous_superfamily

Pfam: PF00018, PF00130, PF07653, PF16664

UniProt features (19 total): strand 9, helix 3, domain 2, region of interest 2, chain 1, zinc finger region 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6B25X-RAY DIFFRACTION2.39
2DL4SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99469-F167.020.31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 198 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, MORF_ITGA2, GOBP_POSITIVE_REGULATION_OF_CATION_CHANNEL_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_TRANSPORTER_ACTIVITY, MORF_BRCA1, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_REGULATION_OF_VOLTAGE_GATED_CALCIUM_CHANNEL_ACTIVITY, GOBP_MULTICELLULAR_ORGANISMAL_MOVEMENT, MEF2_02, GOBP_SKELETAL_MUSCLE_CONTRACTION, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_POSITIVE_REGULATION_OF_TRANSMEMBRANE_TRANSPORT, MORF_RAD51L3, GOBP_MONOATOMIC_CATION_TRANSPORT, SENESE_HDAC1_AND_HDAC2_TARGETS_DN

GO Biological Process (7): skeletal muscle contraction (GO:0003009), signal transduction (GO:0007165), cellular response to heat (GO:0034605), positive regulation of voltage-gated calcium channel activity (GO:1901387), positive regulation of protein localization to plasma membrane (GO:1903078), positive regulation of cation channel activity (GO:2001259), muscle contraction (GO:0006936)

GO Molecular Function (4): zinc ion binding (GO:0008270), transmembrane transporter binding (GO:0044325), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (8): cytosol (GO:0005829), cytoplasmic side of plasma membrane (GO:0009898), T-tubule (GO:0030315), cytoplasm (GO:0005737), plasma membrane (GO:0005886), endomembrane system (GO:0012505), membrane (GO:0016020), sarcolemma (GO:0042383)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
plasma membrane3
striated muscle contraction1
musculoskeletal movement1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
response to heat1
cellular response to stress1
voltage-gated calcium channel activity1
regulation of voltage-gated calcium channel activity1
positive regulation of cation channel activity1
protein localization to plasma membrane1
regulation of protein localization to plasma membrane1
positive regulation of protein localization to cell periphery1
positive regulation of protein localization to membrane1
monoatomic cation channel activity1
positive regulation of ion transmembrane transporter activity1
positive regulation of cation transmembrane transport1
muscle system process1
transition metal ion binding1
protein binding1
binding1
cation binding1
cytoplasm1
cytoplasmic side of membrane1
sarcolemma1
intracellular anatomical structure1
membrane1
cell periphery1
vacuole1

Protein interactions and networks

STRING

1387 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STACHLA-GP17693992
STACTRIM45Q9H8W5907
STACSPARTQ8N0X7889
STACFCHSD2O94868877
STACKIR3DL3Q8N743859
STACKIR2DL1P43626816
STACKIR2DL4P78400794
STACSORBS1Q9BX66775
STACKIR3DL1P43629720
STACKIR3DL2P43630716
STACLILRB1Q8NHL6711
STACLILRB2Q8N423671
STACCACNA1HO95180641
STACCDK2P24941621
STACKIR2DL3P43628594

IntAct

65 interactions, top by confidence:

ABTypeScore
STACYWHAEpsi-mi:“MI:0914”(association)0.730
STACYWHAEpsi-mi:“MI:0407”(direct interaction)0.730
STACYWHAEpsi-mi:“MI:0915”(physical association)0.730
STACSTAT5Bpsi-mi:“MI:0915”(physical association)0.560
NOTCH2NLCSTACpsi-mi:“MI:0915”(physical association)0.560
PAX5STACpsi-mi:“MI:0915”(physical association)0.560
STACLZTS2psi-mi:“MI:0915”(physical association)0.560
GOLGA2STACpsi-mi:“MI:0915”(physical association)0.560
MEOX2STACpsi-mi:“MI:0915”(physical association)0.560
KIAA1958STACpsi-mi:“MI:0915”(physical association)0.560
POU6F2STACpsi-mi:“MI:0915”(physical association)0.560
KANK2STACpsi-mi:“MI:0915”(physical association)0.560
STACNCKIPSDpsi-mi:“MI:0915”(physical association)0.560
STAT5BSTACpsi-mi:“MI:0915”(physical association)0.560
PAX6STACpsi-mi:“MI:0915”(physical association)0.560
STACRNF208psi-mi:“MI:0915”(physical association)0.560
STACATN1psi-mi:“MI:0915”(physical association)0.560
STACFGFR3psi-mi:“MI:0915”(physical association)0.560
KLK6STACpsi-mi:“MI:0915”(physical association)0.560
UBQLN1STACpsi-mi:“MI:0915”(physical association)0.560
PARP2STACpsi-mi:“MI:0557”(adp ribosylation reaction)0.560

BioGRID (41): KANK2 (Two-hybrid), LZTS2 (Two-hybrid), KIAA1958 (Two-hybrid), YWHAZ (Affinity Capture-MS), FBXO11 (Affinity Capture-MS), ANKLE2 (Affinity Capture-MS), STAC (Reconstituted Complex), STAC (Affinity Capture-Western), ANKLE2 (Affinity Capture-MS), YWHAE (Affinity Capture-MS), YWHAZ (Affinity Capture-MS), YWHAB (Affinity Capture-MS), STAC (Biochemical Activity), STAC (Reconstituted Complex), STAC (Two-hybrid)

ESM2 similar proteins: A0A0G2K2P5, A0JNJ1, B1WAP7, G9CGD6, O14640, O75122, O88382, O95049, O97758, P34908, P39447, P51141, P54792, P70175, Q05AS8, Q07157, Q16825, Q5F488, Q5IS48, Q5SGD7, Q5TCQ9, Q5XI81, Q61062, Q62136, Q62728, Q62936, Q6DKE2, Q6P9H4, Q6ZM86, Q812E4, Q86UL8, Q8BMA3, Q8IVH8, Q8JHI3, Q8TDW5, Q920B0, Q924I2, Q925T6, Q92997, Q95168

Diamond homologs: A0JNJ1, A1CEK6, A1DFN5, A2QW93, A4RF61, A6QLK6, A7A261, F1LRS8, O35179, O35964, O43307, O74749, O75791, O75886, O88811, O89100, O93436, P02549, P07751, P09215, P09216, P10830, P13395, P16054, P16086, P16546, P23298, P24723, P28867, P29355, P32793, P34885, P38753, P43603, P53281, P62993, P62994, P70297, P87379, P97306

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance48
Likely benign1
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2207 predictions. Top by Δscore:

VariantEffectΔscore
3:36443395:A:Gacceptor_gain1.0000
3:36443521:G:GTdonor_gain1.0000
3:36484975:A:AGacceptor_gain1.0000
3:36484976:G:GGacceptor_gain1.0000
3:36486132:A:AGacceptor_gain1.0000
3:36486133:G:GAacceptor_gain1.0000
3:36486133:GCC:Gacceptor_gain1.0000
3:36486133:GCCT:Gacceptor_gain1.0000
3:36486245:CCTCT:Cdonor_gain1.0000
3:36486247:TCT:Tdonor_gain1.0000
3:36486250:G:GGdonor_gain1.0000
3:36505741:TTCA:Tacceptor_loss1.0000
3:36505742:TCAG:Tacceptor_loss1.0000
3:36505744:A:AGacceptor_gain1.0000
3:36505744:AG:Aacceptor_gain1.0000
3:36505744:AGG:Aacceptor_gain1.0000
3:36505744:AGGG:Aacceptor_loss1.0000
3:36505745:G:GGacceptor_gain1.0000
3:36505745:GG:Gacceptor_gain1.0000
3:36505745:GGG:Gacceptor_gain1.0000
3:36505745:GGGAT:Gacceptor_gain1.0000
3:36505830:ATGAG:Adonor_loss1.0000
3:36505831:TGAG:Tdonor_loss1.0000
3:36505832:GAGGT:Gdonor_loss1.0000
3:36505833:AG:Adonor_loss1.0000
3:36505834:GGTA:Gdonor_loss1.0000
3:36505835:GT:Gdonor_loss1.0000
3:36505836:T:Gdonor_loss1.0000
3:36528694:A:AGacceptor_gain1.0000
3:36528695:G:GGacceptor_gain1.0000

AlphaMissense

2682 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:36443613:T:CC121R0.999
3:36443614:G:AC121Y0.999
3:36443615:T:GC121W0.999
3:36483018:T:CC139R0.999
3:36486170:T:AL203H0.999
3:36486170:T:CL203P0.999
3:36505789:C:AA292D0.999
3:36528848:G:AG325R0.999
3:36528848:G:CG325R0.999
3:36528848:G:TG325W0.999
3:36443613:T:AC121S0.998
3:36443614:G:CC121S0.998
3:36443622:T:CC124R0.998
3:36483010:G:AG136E0.998
3:36483018:T:AC139S0.998
3:36483019:G:CC139S0.998
3:36483020:C:GC139W0.998
3:36483027:T:CC142R0.998
3:36483028:G:AC142Y0.998
3:36483029:T:GC142W0.998
3:36483078:T:CC159R0.998
3:36484986:T:CF167L0.998
3:36484988:T:AF167L0.998
3:36484988:T:GF167L0.998
3:36484992:C:AR169S0.998
3:36486173:G:CR204P0.998
3:36486179:G:AG206D0.998
3:36505800:T:CF296L0.998
3:36505802:T:AF296L0.998
3:36505802:T:GF296L0.998

dbSNP variants (sampled 300 via entrez): RS1000003058 (3:36480186 A>G), RS1000018457 (3:36500830 C>T), RS1000019737 (3:36383634 A>C), RS1000073444 (3:36383420 C>G), RS1000081813 (3:36461007 C>T), RS1000111430 (3:36461327 T>G), RS1000123294 (3:36416791 G>A), RS1000129980 (3:36545415 A>C), RS1000131748 (3:36458492 A>C,G), RS1000151971 (3:36432811 A>G), RS1000160368 (3:36414248 T>A,C), RS1000163771 (3:36477095 A>T), RS1000183301 (3:36545703 T>G), RS1000184851 (3:36393738 C>T), RS1000205449 (3:36435202 T>G)

Disease associations

OMIM: gene MIM:602317 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

StudyTraitp-value
GCST001572_4Erectile dysfunction in type 1 diabetes4.000000e-06
GCST002112_4Celiac disease6.000000e-06
GCST004739_1Placebo response in major depressive disorder (% change in symptom score)1.000000e-08
GCST004862_181Itch intensity from mosquito bite adjusted by bite size3.000000e-06
GCST004862_42Itch intensity from mosquito bite adjusted by bite size1.000000e-06
GCST005212_5Asthma9.000000e-06
GCST006300_11Smoking behaviour (maximum cigarettes in a 24 hour period)3.000000e-08
GCST007678_1Brooding (response to stress)3.000000e-06
GCST009280_1Kidney disease (end stage renal disease vs non-end stage renal disease) in type 1 diabetes1.000000e-08
GCST009391_1805Metabolite levels8.000000e-06
GCST009391_2090Metabolite levels5.000000e-06
GCST009439_13Age-related cognitive decline (language) (slope of z-scores)3.000000e-07
GCST009444_2Age-related cognitive decline (global cognition) (slope of z-scores)1.000000e-06
GCST010654_1Arterial stiffness (brachial-femoral pulse wave velocity)3.000000e-07

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0008344response to placebo
EFO:0008377mosquito bite reaction itch intensity measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0009264maximum cigarettes per day measurement
EFO:0009858brooding stress response
EFO:0010403triacylglycerol 48:0 measurement
EFO:0010373phosphatidylcholine 32:1 measurement
EFO:0007710cognitive decline measurement
EFO:0004517arterial stiffness measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression3
Benzo(a)pyreneaffects methylation, increases expression, increases methylation3
Valproic Acidaffects expression, decreases methylation2
Aflatoxin B1decreases methylation2
Particulate Matterincreases abundance, increases expression, decreases expression2
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amineincreases expression1
bisphenol Adecreases methylation1
lead acetateincreases expression1
trichostatin Aincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydeincreases expression1
cadmium acetateincreases expression1
aflatoxin B2decreases methylation1
nickel sulfatedecreases expression1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidincreases expression1
jinfukangaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Vorinostatincreases expression1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Calcitriolincreases expression1
Carbamazepineaffects expression1
Cisplatinaffects cotreatment, decreases expression1
Copperdecreases expression, affects cotreatment1
Melphalandecreases expression1
Nicotineincreases expression1

Clinical trials (associated diseases)

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