DSN1

gene
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Also known as dJ469A13.2MIS13KNL3hKNL-3

Summary

DSN1 (DSN1 component of MIS12 kinetochore complex, HGNC:16165) is a protein-coding gene on chromosome 20q11.23, encoding Kinetochore-associated protein DSN1 homolog (Q9H410). Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis. It is a selective cancer dependency (DepMap: 89.5% of cell lines).

This gene encodes a kinetochore protein that functions as part of the minichromosome instability-12 centromere complex. The encoded protein is required for proper kinetochore assembly and progression through the cell cycle. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 79980 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 57 total
  • Cancer dependency (DepMap): dependent in 89.5% of screened cell lines
  • MANE Select transcript: NM_001145315

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16165
Approved symbolDSN1
NameDSN1 component of MIS12 kinetochore complex
Location20q11.23
Locus typegene with protein product
StatusApproved
AliasesdJ469A13.2, MIS13, KNL3, hKNL-3
Ensembl geneENSG00000149636
Ensembl biotypeprotein_coding
OMIM609175
Entrez79980

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 27 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000373734, ENST00000373740, ENST00000373750, ENST00000426836, ENST00000438549, ENST00000447406, ENST00000448110, ENST00000473615, ENST00000480153, ENST00000492703, ENST00000863304, ENST00000863305, ENST00000863306, ENST00000863307, ENST00000863308, ENST00000863309, ENST00000925982, ENST00000925983, ENST00000925984, ENST00000925985, ENST00000925986, ENST00000925987, ENST00000925988, ENST00000925989, ENST00000925990, ENST00000925991, ENST00000925992, ENST00000925993, ENST00000963378, ENST00000963379

RefSeq mRNA: 5 — MANE Select: NM_001145315 NM_001145315, NM_001145316, NM_001145317, NM_001145318, NM_024918

CCDS: CCDS13286, CCDS46596, CCDS46597

Canonical transcript exons

ENST00000373750 — 11 exons

ExonStartEnd
ENSE000018894553677366236773763
ENSE000034602153676796936768042
ENSE000035003933676676936766841
ENSE000035086373676246136762548
ENSE000035255513675568236755829
ENSE000035267233675476336754850
ENSE000035580303677142536771473
ENSE000035754203677087336771193
ENSE000036124063675855836758617
ENSE000036862693675179536752897
ENSE000037840633675808736758161

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 93.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.0521 / max 110.7990, expressed in 1752 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
18714112.05211752

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.90gold quality
ventricular zoneUBERON:000305391.44gold quality
right testisUBERON:000453488.77gold quality
secondary oocyteCL:000065588.34gold quality
left testisUBERON:000453388.28gold quality
ganglionic eminenceUBERON:000402387.00gold quality
testisUBERON:000047386.53gold quality
oocyteCL:000002386.45gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.39gold quality
rectumUBERON:000105284.27gold quality
right adrenal gland cortexUBERON:003582783.94gold quality
adrenal tissueUBERON:001830382.87gold quality
right adrenal glandUBERON:000123382.63gold quality
mucosa of transverse colonUBERON:000499182.42gold quality
left adrenal gland cortexUBERON:003582582.17gold quality
granulocyteCL:000009481.35gold quality
left adrenal glandUBERON:000123481.31gold quality
adrenal cortexUBERON:000123580.72gold quality
stromal cell of endometriumCL:000225580.65gold quality
adrenal glandUBERON:000236980.36gold quality
calcaneal tendonUBERON:000370180.24gold quality
lymph nodeUBERON:000002979.76gold quality
spleenUBERON:000210679.74gold quality
embryoUBERON:000092279.42gold quality
descending thoracic aortaUBERON:000234578.89gold quality
esophagus mucosaUBERON:000246978.81gold quality
right lungUBERON:000216778.50gold quality
skin of legUBERON:000151178.46gold quality
bone marrow cellCL:000209278.42gold quality
skin of abdomenUBERON:000141678.40gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

50 targeting DSN1, 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-513A-5P100.0069.772465
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-477599.9875.006394
HSA-MIR-50799.9770.111915
HSA-MIR-60799.9773.625593
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-335-3P99.9373.364958
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-153-5P99.8973.866317
HSA-MIR-579-3P99.8671.663628
HSA-MIR-369-3P99.8570.522264
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-132399.8369.892471
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-498-5P99.7669.641807
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-425599.7267.701541
HSA-MIR-128499.6773.561353
HSA-MIR-315399.5567.592337
HSA-MIR-5004-3P99.5468.271371
HSA-MIR-443799.5265.291266
HSA-MIR-1212399.5271.792990
HSA-MIR-6727-3P99.4965.921333
HSA-MIR-312399.4767.152693

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 89.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • HsMis13 phosphorylation by Aurora B is required for organizing a stable bi-oriented microtubule kinetochore attachment that is essential for faithful chromosome segregation in mitosis. (PMID:18640974)
  • this report provides clear evidence that overexpression of the AURKA, SKA3, and DSN1 genes strongly correlates with the progression of colorectal adenomas to colorectal cancer (PMID:27329586)
  • DSN1 is overexpressed in hepatocellular carcinoma tissues and strongly associated with poor prognosis. (PMID:30136646)
  • Identification of CDCA8, DSN1 and BIRC5 in Regulating Cell Cycle and Apoptosis in Osteosarcoma Using Bioinformatics and Cell Biology. (PMID:33153400)
  • DSN1 is a prognostic biomarker and correlated with clinical characterize in breast cancer. (PMID:34238686)
  • SRSF9 promotes colorectal cancer progression via stabilizing DSN1 mRNA in an m6A-related manner. (PMID:35509101)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriodsn1ENSDARG00000089922
mus_musculusDsn1ENSMUSG00000027635
rattus_norvegicusDsn1ENSRNOG00000006236

Protein

Protein identifiers

Kinetochore-associated protein DSN1 homologQ9H410 (reviewed: Q9H410)

All UniProt accessions (4): Q9H410, Q5JW53, Q5JW54, Q5JW57

UniProt curated annotations — full annotation on UniProt →

Function. Part of the MIS12 complex which is required for normal chromosome alignment and segregation and kinetochore formation during mitosis.

Subunit / interactions. Component of the MIS12 complex composed of MIS12, DSN1, NSL1 and PMF1. Also interacts with KNL1, CBX3 and CBX5. Interacts with KNSTRN.

Subcellular location. Nucleus. Chromosome. Centromere. Kinetochore.

Isoforms (4)

UniProt IDNamesCanonical?
Q9H410-11yes
Q9H410-22
Q9H410-44
Q9H410-33

RefSeq proteins (5): NP_001138787, NP_001138788, NP_001138789, NP_001138790, NP_079194 (=MANE)

Domains & families (InterPro)

IDNameType
IPR013218Dsn1/Mis13Family

Pfam: PF08202

UniProt features (31 total): helix 11, modified residue 8, splice variant 3, region of interest 2, compositionally biased region 2, chain 1, cross-link 1, sequence conflict 1, strand 1, turn 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
5LSIX-RAY DIFFRACTION2
8PPRELECTRON MICROSCOPY3
5LSJX-RAY DIFFRACTION3.25
5LSKX-RAY DIFFRACTION3.5
8Q5HELECTRON MICROSCOPY4.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H410-F168.280.32

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 (9): 109, 125, 331, 253, 28, 30, 58, 77, 81

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-141444Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-2467813Separation of Sister Chromatids
R-HSA-2500257Resolution of Sister Chromatid Cohesion
R-HSA-5663220RHO GTPases Activate Formins
R-HSA-6798695Neutrophil degranulation
R-HSA-68877Mitotic Prometaphase
R-HSA-9648025EML4 and NUDC in mitotic spindle formation

MSigDB gene sets: 151 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GOBP_ATTACHMENT_OF_SPINDLE_MICROTUBULES_TO_KINETOCHORE, REACTOME_INNATE_IMMUNE_SYSTEM, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOCC_SECRETORY_GRANULE, GOBP_CHROMOSOME_LOCALIZATION, GOBP_MUSCLE_CELL_PROLIFERATION, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_STRIATED_MUSCLE_CELL_PROLIFERATION, FISCHER_DREAM_TARGETS, chr20q11, ACEVEDO_LIVER_CANCER_UP, GOBP_ORGANELLE_LOCALIZATION, KOBAYASHI_EGFR_SIGNALING_24HR_DN, REACTOME_CELL_CYCLE_CHECKPOINTS

GO Biological Process (4): attachment of spindle microtubules to kinetochore (GO:0008608), skeletal muscle satellite cell proliferation (GO:0014841), cell division (GO:0051301), chromosome segregation (GO:0007059)

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

GO Cellular Component (14): MIS12/MIND type complex (GO:0000444), kinetochore (GO:0000776), spindle pole (GO:0000922), outer kinetochore (GO:0000940), fibrillar center (GO:0001650), extracellular region (GO:0005576), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), nuclear body (GO:0016604), azurophil granule lumen (GO:0035578), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Mitotic Prometaphase2
Amplification of signal from the kinetochores1
Mitotic Anaphase1
RHO GTPase Effectors1
Innate Immune System1
M Phase1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
intracellular membraneless organelle4
cell cycle process2
nuclear lumen2
microtubule binding1
metaphase chromosome alignment1
skeletal muscle cell proliferation1
cellular process1
binding1
outer kinetochore1
condensed chromosome, centromeric region1
supramolecular complex1
spindle1
kinetochore1
protein-containing complex1
nucleolus1
intracellular membrane-bounded organelle1
cytoplasm1
nucleoplasm1
vacuolar lumen1
secretory granule lumen1
azurophil granule1
chromosomal region1

Protein interactions and networks

STRING

1801 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DSN1PMF1Q6P1K2998
DSN1A0A087WT04A0A087WT04998
DSN1NSL1Q96IY1987
DSN1MIS12Q9H081984
DSN1ZWINTO95229949
DSN1KNL1Q8NG31948
DSN1CENPAP49450899
DSN1SPC24Q8NBT2899
DSN1CENPCQ03188890
DSN1CBX5P45973888
DSN1CENPTQ96BT3816
DSN1INCENPQ9NQS7807
DSN1NUF2Q9BZD4806
DSN1CENPIQ92674798
DSN1AURKBQ96GD4797

IntAct

132 interactions, top by confidence:

ABTypeScore
ZWINTNDC80psi-mi:“MI:0914”(association)0.940
SPC25NDC80psi-mi:“MI:0914”(association)0.940
DSN1MIS12psi-mi:“MI:2364”(proximity)0.930
MIS12DSN1psi-mi:“MI:2364”(proximity)0.930
MIS12DSN1psi-mi:“MI:0915”(physical association)0.930
DSN1MIS12psi-mi:“MI:0915”(physical association)0.930
SPC24NDC80psi-mi:“MI:0914”(association)0.920
DSN1NSL1psi-mi:“MI:2364”(proximity)0.920
NSL1DSN1psi-mi:“MI:2364”(proximity)0.920
NSL1DSN1psi-mi:“MI:0915”(physical association)0.920
DSN1NSL1psi-mi:“MI:0915”(physical association)0.920

BioGRID (233): DSN1 (Affinity Capture-RNA), DSN1 (Affinity Capture-RNA), DSN1 (Affinity Capture-MS), DSN1 (Affinity Capture-MS), DSN1 (Affinity Capture-MS), DSN1 (Affinity Capture-MS), DSN1 (Affinity Capture-MS), RNF20 (Affinity Capture-MS), RNF40 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), SPC25 (Affinity Capture-MS), EXOC7 (Affinity Capture-MS), BRCA2 (Affinity Capture-MS), SPC24 (Affinity Capture-MS), NDC80 (Affinity Capture-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A1L2Y1, A2ALV5, A9JRX0, B2GUZ2, D3ZSP7, F1QB81, O35892, O70608, O75113, P23497, P70347, Q0P5X5, Q13129, Q16533, Q2T9I9, Q3U1D0, Q5CZC0, Q5H9M0, Q5REF4, Q5RHB5, Q5SW75, Q5T4T6, Q5T5J6, Q5XG69, Q5ZLE9, Q60664, Q63HN8, Q7M6U3, Q7Z4H7, Q80VH0, Q8BVK9, Q8C263, Q8CCC3, Q8NA03, Q90WN7, Q92844, Q96QP1

Diamond homologs: Q9CYC5, Q9H410

SIGNOR signaling

4 interactions.

AEffectBMechanism
AURKBdown-regulatesDSN1phosphorylation
UBR2“down-regulates quantity”DSN1ubiquitination
DSN1“form complex”“MIS12 complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 84 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Amplification of signal from the kinetochores930.6×7e-10
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal1428.1×2e-14
Mitotic Spindle Checkpoint924.6×4e-09
EML4 and NUDC in mitotic spindle formation1422.4×1e-13
Resolution of Sister Chromatid Cohesion1420.9×3e-13
RHO GTPases Activate Formins1520.1×9e-14
Cell Cycle Checkpoints1116.8×2e-09
Mitotic Prometaphase1416.7×6e-12

GO biological processes:

GO termPartnersFoldFDR
attachment of spindle microtubules to kinetochore8101.2×2e-12
mitotic spindle assembly checkpoint signaling753.1×9e-09
mitotic sister chromatid segregation639.0×1e-06
chromosome segregation818.8×1e-06
cell division159.4×9e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance35
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1526 predictions. Top by Δscore:

VariantEffectΔscore
20:36752893:CTTTC:Cacceptor_gain1.0000
20:36752894:TTTC:Tacceptor_gain1.0000
20:36752895:TTC:Tacceptor_gain1.0000
20:36752896:TC:Tacceptor_gain1.0000
20:36752896:TCCT:Tacceptor_loss1.0000
20:36752897:CC:Cacceptor_gain1.0000
20:36752897:CCTGC:Cacceptor_loss1.0000
20:36752898:C:CAacceptor_loss1.0000
20:36752898:C:CCacceptor_gain1.0000
20:36754757:GCTTA:Gdonor_loss1.0000
20:36754758:CTTAC:Cdonor_loss1.0000
20:36754759:TTA:Tdonor_loss1.0000
20:36754760:T:TGdonor_loss1.0000
20:36754761:A:ACdonor_gain1.0000
20:36754761:ACCGA:Adonor_loss1.0000
20:36754762:C:CCdonor_gain1.0000
20:36754762:C:Tdonor_loss1.0000
20:36754762:CCGAG:Cdonor_gain1.0000
20:36754766:G:Cdonor_gain1.0000
20:36754792:TGGG:Tdonor_gain1.0000
20:36754801:T:Adonor_gain1.0000
20:36754846:TCCAT:Tacceptor_gain1.0000
20:36754847:CCAT:Cacceptor_gain1.0000
20:36754847:CCATC:Cacceptor_gain1.0000
20:36754848:CAT:Cacceptor_gain1.0000
20:36754848:CATC:Cacceptor_gain1.0000
20:36754848:CATCT:Cacceptor_loss1.0000
20:36754849:AT:Aacceptor_gain1.0000
20:36754849:ATCTG:Aacceptor_loss1.0000
20:36754850:TC:Tacceptor_loss1.0000

AlphaMissense

2338 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:36767975:A:CS141R0.993
20:36767975:A:TS141R0.993
20:36767977:T:GS141R0.993
20:36758139:A:GW225R0.989
20:36758139:A:TW225R0.989
20:36767988:A:GL137P0.981
20:36758137:C:AW225C0.980
20:36758137:C:GW225C0.980
20:36768000:C:GR133P0.977
20:36754840:A:GL295P0.975
20:36754819:A:GL302P0.973
20:36766825:A:GL149P0.971
20:36766839:G:CF144L0.970
20:36766839:G:TF144L0.970
20:36766841:A:GF144L0.970
20:36755742:T:AK271N0.964
20:36755742:T:GK271N0.964
20:36758129:A:GL228P0.963
20:36767985:A:GL138P0.962
20:36754797:A:CS309R0.957
20:36754797:A:TS309R0.957
20:36754799:T:GS309R0.957
20:36770928:A:CS100R0.957
20:36770928:A:TS100R0.957
20:36770930:T:GS100R0.957
20:36766794:G:CF159L0.956
20:36766794:G:TF159L0.956
20:36766796:A:GF159L0.956
20:36767973:A:GF142S0.949
20:36766780:A:GF164S0.946

dbSNP variants (sampled 300 via entrez): RS1000191120 (20:36763905 A>AAG), RS1000251492 (20:36762224 A>C), RS1000312909 (20:36768630 G>T), RS1000363646 (20:36760946 G>A,C), RS1000376783 (20:36769003 C>T), RS1000396277 (20:36760765 G>A), RS1000485227 (20:36761904 G>C), RS1000723548 (20:36774556 C>T), RS1000755230 (20:36774276 A>G), RS1000910599 (20:36756547 T>A,C), RS1000982305 (20:36757173 T>A,G), RS1001427832 (20:36753217 G>A,T), RS1001594663 (20:36752510 G>A), RS1001626759 (20:36768519 G>T), RS1001743870 (20:36766963 C>A,G)

Disease associations

OMIM: gene MIM:609175 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST007401_21Factor VII activity7.000000e-07
GCST009847_9Hallux valgus3.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004619factor VII measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
Tetrachlorodibenzodioxinaffects expression, decreases expression3
Cyclosporinedecreases expression3
bisphenol Aaffects expression, decreases expression2
Resveratrolaffects cotreatment, increases expression2
Air Pollutantsaffects cotreatment, affects expression, increases abundance, decreases expression2
Arsenicincreases expression, affects cotreatment, decreases expression, increases abundance2
Benzo(a)pyreneincreases expression, increases mutagenesis2
Cisplatinaffects cotreatment, increases expression2
Estradioldecreases reaction, increases expression, decreases expression2
Valproic Acidaffects expression, decreases expression2
FR900359affects phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
testosterone enanthateaffects expression1
alpha-pineneaffects cotreatment, affects expression, increases abundance1
propionaldehydedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
zinc chromatedecreases expression, increases abundance1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, increases expression1
coumarindecreases phosphorylation1
methacrylaldehydeaffects cotreatment, affects expression, increases abundance1
chromium hexavalent iondecreases expression, increases abundance1
abrinedecreases expression1
jinfukangaffects cotreatment, increases expression1
incobotulinumtoxinAdecreases expression1
Dasatinibdecreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases 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.