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FSD1

gene
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Also known as MGC3213MIR1

Summary

FSD1 (fibronectin type III and SPRY domain containing 1, HGNC:13745) is a protein-coding gene on chromosome 19p13.3, encoding Fibronectin type III and SPRY domain-containing protein 1 (Q9BTV5). May be involved in microtubule organization and stabilization.

This gene encodes a centrosome associated protein that is characterized by an N-terminal coiled-coil region downstream of B-box (BBC) domain, a central fibronectin type III domain, and a C-terminal repeats in splA and RyR (SPRY) domain. The encoded protein associates with a subset of microtubules and may be involved in the stability and organization of microtubules during cytokinesis.

Source: NCBI Gene 79187 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 83 total
  • MANE Select transcript: NM_024333

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13745
Approved symbolFSD1
Namefibronectin type III and SPRY domain containing 1
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesMGC3213, MIR1
Ensembl geneENSG00000105255
Ensembl biotypeprotein_coding
OMIM609828
Entrez79187

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 15 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000221856, ENST00000594438, ENST00000597480, ENST00000597590, ENST00000598010, ENST00000598179, ENST00000599375, ENST00000601006, ENST00000601678, ENST00000601815, ENST00000859934, ENST00000911581, ENST00000911582, ENST00000911583, ENST00000911584, ENST00000911585, ENST00000911586, ENST00000911587, ENST00000965757, ENST00000965758

RefSeq mRNA: 2 — MANE Select: NM_024333 NM_001330429, NM_024333

CCDS: CCDS12127, CCDS82277

Canonical transcript exons

ENST00000221856 — 13 exons

ExonStartEnd
ENSE0000137168743045984304761
ENSE0000320480443235334323836
ENSE0000353914643171824317280
ENSE0000355401243233484323436
ENSE0000358757743061984306329
ENSE0000359213443059464306041
ENSE0000359996343183464318505
ENSE0000360853643188724318951
ENSE0000363340043229864323237
ENSE0000364856743118424312051
ENSE0000365050443104754310596
ENSE0000367145043078824307983
ENSE0000368386543102734310295

Expression profiles

Bgee: expression breadth ubiquitous, 188 present calls, max score 95.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.6380 / max 80.3774, expressed in 1190 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1733304.0714988
1733292.3717897
1733310.1950110

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right frontal lobeUBERON:000281095.36gold quality
right hemisphere of cerebellumUBERON:001489095.33gold quality
cerebellar hemisphereUBERON:000224595.09gold quality
cerebellar cortexUBERON:000212994.92gold quality
cortical plateUBERON:000534393.99gold quality
anterior cingulate cortexUBERON:000983593.64gold quality
cingulate cortexUBERON:000302793.54gold quality
Brodmann (1909) area 9UBERON:001354093.25gold quality
cerebellumUBERON:000203793.24gold quality
prefrontal cortexUBERON:000045192.74gold quality
dorsolateral prefrontal cortexUBERON:000983492.65gold quality
ganglionic eminenceUBERON:000402392.46gold quality
neocortexUBERON:000195091.90gold quality
frontal cortexUBERON:000187091.61gold quality
amygdalaUBERON:000187690.87gold quality
cerebral cortexUBERON:000095690.75gold quality
ventricular zoneUBERON:000305390.53gold quality
primary visual cortexUBERON:000243689.80gold quality
telencephalonUBERON:000189389.26gold quality
middle temporal gyrusUBERON:000277188.89gold quality
C1 segment of cervical spinal cordUBERON:000646988.78gold quality
hypothalamusUBERON:000189888.74gold quality
Ammon’s hornUBERON:000195488.69gold quality
nucleus accumbensUBERON:000188288.09gold quality
caudate nucleusUBERON:000187388.01gold quality
temporal lobeUBERON:000187187.85gold quality
brainUBERON:000095587.80gold quality
putamenUBERON:000187487.69gold quality
forebrainUBERON:000189087.63gold quality
spinal cordUBERON:000224086.23gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-GEOD-110499no2.88
E-ANND-3no2.09

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MEF2C, MYOD1, PAX7

miRNA regulators (miRDB)

12 targeting FSD1, 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-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-424-5P99.8971.902641
HSA-MIR-6838-5P99.8971.942690
HSA-MIR-613499.6365.681537
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-66199.0965.942062
HSA-MIR-4477A98.8369.752952
HSA-MIR-6759-3P96.9468.31823

Literature-anchored findings (GeneRIF, showing 6)

  • Data report the identification of MIR1, a protein with microtubule-binding activity which is located at the centrosome and is related to MID1/midin. [MIR1] (PMID:12154070)
  • Taken together, our findings established a tumor suppressive role for miR-1 in the progression of ccRCC by targeting CDK4, CDK6, Caprin1 and Slug and suggested miR-1 can be served as a novel potential therapeutic target for ccRCC. (PMID:26036633)
  • These regulatory mechanisms of miR-1 expression could help us to understand the functions of altered miR-1 expression. (PMID:27923712)
  • Overexpression of miR-1 mimics significantly decreased tumor glycolysis, including lactate production and glucose uptake, and cell proliferation, and these effects were reversed by ectopic expression of Smad3. (PMID:28471448)
  • The centrosome protein FSD1 anchors microtubule asters to interphase centrosomes by binding to microtubules. (PMID:30538248)
  • Proliferation of PC cells by targeting the c-Met/Akt/mTOR signaling pathway. (PMID:30551391)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriofsd1ENSDARG00000062017
mus_musculusFsd1ENSMUSG00000011589
rattus_norvegicusFsd1ENSRNOG00000050318

Paralogs (3): FSD1L (ENSG00000106701), CMYA5 (ENSG00000164309), FSD2 (ENSG00000186628)

Protein

Protein identifiers

Fibronectin type III and SPRY domain-containing protein 1 — Q9BTV5 (reviewed: Q9BTV5)

Alternative names: MID1-related protein 1, Microtubule-associated protein GLFND

All UniProt accessions (5): Q9BTV5, M0QY68, M0R1R0, M0R2F6, M0R366

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in microtubule organization and stabilization.

Subunit / interactions. Oligomerization is required for binding to microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Nucleus. Cleavage furrow.

Tissue specificity. Highly expressed in brain tissues, including cerebellum, cerebral cortex, medulla, occipital pole, frontal lobe, temporal lobe and putamen. Lower expression in spinal cord.

Domain organisation. B30.2 box contains a microtubule-binding site.

RefSeq proteins (2): NP_001317358, NP_077309* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001870B30.2/SPRYDomain
IPR003649Bbox_CDomain
IPR003877SPRY_domDomain
IPR003961FN3_domDomain
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR013783Ig-like_foldHomologous_superfamily
IPR017903COS_domainDomain
IPR035742SPRY/PRY_FSD1Domain
IPR036116FN3_sfHomologous_superfamily
IPR043136B30.2/SPRY_sfHomologous_superfamily
IPR050617E3_ligase_FN3/SPRYFamily

Pfam: PF00041, PF00622

UniProt features (18 total): mutagenesis site 8, domain 3, modified residue 2, chain 1, sequence conflict 1, region of interest 1, coiled-coil region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BTV5-F188.120.75

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 (2): 310, 320

Mutagenesis-validated functional residues (8):

PositionPhenotype
313reduced ability to associate with microtubules; when associated with d-317; e-322 and d-324.
317in mitosis, remained associated with microtubules; when associated with a-313; a-322 and a-324.
317reduced ability to associate with microtubules; when associated with d-313; e-322 and d-324.
322in mitosis, remained associated with microtubules; when associated with a-313; a-317 and a-324.
322reduced ability to associate with microtubules; when associated with d-313; d-317 and d-324.
324in mitosis, remained associated with microtubules; when associated with a-313; a-317 and a-322.
324reduced ability to associate with microtubules; when associated with d-313; d-317 and e-322.
313in mitosis, remained associated with microtubules; when associated with a-317; a-322 and a-324.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): HORIUCHI_WTAP_TARGETS_DN, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_CYTOKINESIS, GOBP_REGULATION_OF_SPINDLE_ORGANIZATION, GOBP_REGULATION_OF_CELL_CYCLE, MARTIN_NFKB_TARGETS_UP, MARTIN_VIRAL_GPCR_SIGNALING_UP, GOCC_CENTROSOME, GOBP_REGULATION_OF_CYTOKINESIS, GOBP_REGULATION_OF_CELL_DIVISION, GOZGIT_ESR1_TARGETS_UP, GOBP_MITOTIC_CELL_CYCLE

GO Biological Process (5): cytoplasmic microtubule organization (GO:0031122), regulation of cytokinesis (GO:0032465), cell division (GO:0051301), regulation of cell division (GO:0051302), regulation of mitotic spindle organization (GO:0060236)

GO Molecular Function (3): microtubule binding (GO:0008017), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (7): nucleus (GO:0005634), centrosome (GO:0005813), cytosol (GO:0005829), microtubule (GO:0005874), cleavage furrow (GO:0032154), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
microtubule cytoskeleton organization1
supramolecular fiber organization1
cytokinesis1
regulation of cell cycle process1
regulation of cell division1
cellular process1
regulation of cellular process1
cell division1
mitotic spindle organization1
regulation of spindle organization1
tubulin binding1
protein binding1
binding1
intracellular membrane-bounded organelle1
centriole1
microtubule organizing center1
cytoplasm1
microtubule cytoskeleton1
polymeric cytoskeletal fiber1
cell division site1
plasma membrane region1
intracellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

572 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FSD1TUBG1P23258549
FSD1BBOX1O75936548
FSD1SCRN1Q12765521
FSD1BCL7AQ4VC05513
FSD1JAKMIP2Q96AA8509
FSD1FN1P02751497
FSD1FSTL3O95633468
FSD1MARK1Q9P0L2464
FSD1CDK5Q00535442
FSD1TUBB3Q13509417
FSD1TP73O15350408
FSD1C11orf86A6NJI1398
FSD1TGFBIQ15582397
FSD1CHIT1Q13231395
FSD1COL6A3P12111388

IntAct

26 interactions, top by confidence:

ABTypeScore
FSD1UBFD1psi-mi:“MI:0914”(association)0.530
DISC1AP4M1psi-mi:“MI:0914”(association)0.530
PEX14FSD1psi-mi:“MI:0407”(direct interaction)0.440
FSD1PKMpsi-mi:“MI:0217”(phosphorylation reaction)0.440
ENGIGKV2-28psi-mi:“MI:0914”(association)0.350
YWHAHSHTN1psi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
HCN1USP27Xpsi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
FTLSH3PXD2Bpsi-mi:“MI:0914”(association)0.350
KRT16NEFMpsi-mi:“MI:0914”(association)0.350
VCPSHTN1psi-mi:“MI:0914”(association)0.350
VCPFAM171A2psi-mi:“MI:0914”(association)0.350
SCLT1VWA8psi-mi:“MI:2364”(proximity)0.270
SCLT1ABLIM1psi-mi:“MI:2364”(proximity)0.270
MAPTDCTN6psi-mi:“MI:2364”(proximity)0.270
PPP1R16AFSD1psi-mi:“MI:0915”(physical association)0.000
FSD1NAP1L1psi-mi:“MI:0915”(physical association)0.000

BioGRID (130): SPECC1L (Affinity Capture-MS), TLDC1 (Affinity Capture-MS), AGFG1 (Affinity Capture-MS), PYGB (Affinity Capture-MS), MIB1 (Affinity Capture-MS), AIDA (Affinity Capture-MS), SRC (Affinity Capture-MS), SNCA (Affinity Capture-MS), BIRC2 (Affinity Capture-MS), UBE2D2 (Affinity Capture-MS), SERPINB1 (Affinity Capture-MS), NAA50 (Affinity Capture-MS), UBE2E3 (Affinity Capture-MS), ETF1 (Affinity Capture-MS), FBXO46 (Affinity Capture-MS)

ESM2 similar proteins: A1A5C7, A6NCF5, A6QLN9, A8MUP2, D3YYU8, D3ZZ80, F1LTR1, O75147, O88843, P08887, Q28D01, Q3SZQ2, Q3UHH2, Q3ZCW2, Q4R539, Q5EA19, Q5R4Q7, Q5R5K6, Q5RCI5, Q5RFN0, Q5SP67, Q5ZHQ2, Q642A6, Q67FW5, Q6AZB0, Q6IA17, Q6PCB0, Q7TPB4, Q86TI4, Q86VF2, Q8BGR6, Q8BZI6, Q8C6G8, Q8N5I2, Q8N653, Q8R2Z5, Q8VE98, Q8VED9, Q969P0, Q96NJ5

Diamond homologs: A0A2P1BRP3, A0A2P1BRQ0, A0ZSK3, A0ZSK4, O70583, O95361, Q05B84, Q14258, Q1XHU0, Q309B1, Q4R539, Q5R760, Q61510, Q6MFZ5, Q7TPM6, Q8BVW3, Q8BYN5, Q91453, Q98989, Q98993, Q99PP9, Q9BTV5, Q9BXM9, Q9ESN2, Q9HCM9, Q9Y577, A0JN74, A4QPC6, A6NGJ6, A6NI03, A6NK02, A6NLI5, A6NLU0, B1H278, C9J1S8, F4I443, F8VTS6, O00478, O00481, O15344

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign4
Benign6

Top pathogenic / likely-pathogenic (0)

SpliceAI

2213 predictions. Top by Δscore:

VariantEffectΔscore
19:4304750:G:GTdonor_gain1.0000
19:4304758:GAGG:Gdonor_gain1.0000
19:4305930:A:AGacceptor_gain1.0000
19:4305938:T:TAacceptor_gain1.0000
19:4305942:GCA:Gacceptor_loss1.0000
19:4305943:CA:Cacceptor_loss1.0000
19:4305944:A:ACacceptor_loss1.0000
19:4306181:T:TAacceptor_gain1.0000
19:4306185:T:Aacceptor_gain1.0000
19:4306190:C:CAacceptor_gain1.0000
19:4306326:GCAG:Gdonor_gain1.0000
19:4306327:CAGGT:Cdonor_loss1.0000
19:4306328:AGGTG:Adonor_loss1.0000
19:4306329:GGTG:Gdonor_loss1.0000
19:4306330:G:GGdonor_gain1.0000
19:4307870:T:TAacceptor_gain1.0000
19:4307871:G:Aacceptor_gain1.0000
19:4307875:T:Gacceptor_gain1.0000
19:4307877:CACA:Cacceptor_loss1.0000
19:4307879:CAGAA:Cacceptor_loss1.0000
19:4307880:A:AGacceptor_gain1.0000
19:4307880:A:Cacceptor_loss1.0000
19:4307881:G:GAacceptor_gain1.0000
19:4307881:G:GTacceptor_loss1.0000
19:4307881:GA:Gacceptor_gain1.0000
19:4307881:GAA:Gacceptor_gain1.0000
19:4307881:GAACC:Gacceptor_gain1.0000
19:4307982:AG:Adonor_loss1.0000
19:4307983:GG:Gdonor_loss1.0000
19:4307984:G:GCdonor_loss1.0000

AlphaMissense

3272 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:4311907:T:AW186R1.000
19:4311907:T:CW186R1.000
19:4318388:T:CL281P1.000
19:4318414:T:AW290R1.000
19:4318414:T:CW290R1.000
19:4318946:T:AV345D1.000
19:4306325:T:CL80P0.999
19:4311950:T:CL200P0.999
19:4318416:G:CW290C0.999
19:4318416:G:TW290C0.999
19:4318924:T:CF338L0.999
19:4318926:C:AF338L0.999
19:4318926:C:GF338L0.999
19:4318951:G:TG347W0.999
19:4322986:G:AG347E0.999
19:4323018:T:AW358R0.999
19:4323018:T:CW358R0.999
19:4323047:G:CK367N0.999
19:4323047:G:TK367N0.999
19:4323060:G:CG372R0.999
19:4323099:G:CG385R0.999
19:4323100:G:AG385D0.999
19:4323100:G:TG385V0.999
19:4323117:T:AW391R0.999
19:4323117:T:CW391R0.999
19:4323160:C:AA405D0.999
19:4323426:C:AP457H0.999
19:4323429:C:AA458D0.999
19:4323432:T:CF459S0.999
19:4307939:G:CA101P0.998

dbSNP variants (sampled 300 via entrez): RS1000028241 (19:4308891 C>G,T), RS1000035569 (19:4306916 G>A,T), RS1000199429 (19:4309186 T>C), RS1000303847 (19:4314576 T>C), RS1000474710 (19:4310256 T>C), RS1000621976 (19:4305791 T>C), RS1000871870 (19:4321051 G>A,C), RS1000925063 (19:4315090 G>A), RS1000993923 (19:4305505 A>T), RS1001287443 (19:4316479 C>G,T), RS1001527985 (19:4306474 T>C,G), RS1001600354 (19:4322924 A>G), RS1001746895 (19:4311371 A>G,T), RS1001909700 (19:4323773 A>G,T), RS1002028151 (19:4318818 G>A)

Disease associations

OMIM: gene MIM:609828 | 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):

StudyTraitp-value
GCST005024_89Pursuit maintenance gain2.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0008433pursuit maintenance gain measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression3
Particulate Matterincreases abundance, increases expression, decreases expression2
aristolochic acid Iincreases expression1
GSK-J4decreases expression1
bufotalindecreases expression1
bisphenol Adecreases methylation1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
butyraldehydeincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxalinedecreases expression1
beta-methylcholineaffects expression1
pentanalincreases expression1
di-n-butylphosphoric acidaffects expression1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
azoxystrobindecreases expression1
jinfukangaffects cotreatment, increases expression1
picoxystrobindecreases expression1
Decitabineincreases expression1
Sunitinibincreases expression1
Air Pollutantsincreases abundance, decreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Vehicle Emissionsincreases expression1
Benzo(a)pyreneaffects methylation1
Cisplatinaffects cotreatment, increases expression1
Estradiolaffects cotreatment, increases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Phthalic Acidsdecreases expression1
Rotenonedecreases expression1
Smokedecreases expression1
Tretinoindecreases expression1

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot