KNL1

Summary

KNL1 (kinetochore scaffold 1, HGNC:24054) is a protein-coding gene on chromosome 15q15.1, encoding Outer kinetochore KNL1 complex subunit KNL1 (Q8NG31). Acts as a component of the outer kinetochore KNL1 complex that serves as a docking point for spindle assembly checkpoint components and mediates microtubule-kinetochore interactions. It is a selective cancer dependency (DepMap: 77.4% of cell lines).

The protein encoded by this gene is a component of the multiprotein assembly that is required for creation of kinetochore-microtubule attachments and chromosome segregation. The encoded protein functions as a scaffold for proteins that influence the spindle assembly checkpoint during the eukaryotic cell cycle and it interacts with at least five different kinetochore proteins and two checkpoint kinases. In adults, this gene is predominantly expressed in normal testes, various cancer cell lines and primary tumors from other tissues and is ubiquitously expressed in fetal tissues. This gene was originally identified as a fusion partner with the mixed-lineage leukemia (MLL) gene in t(11;15)(q23;q14). Mutations in this gene cause autosomal recessive primary microcephaly-4 (MCPH4). Alternative splicing results in multiple transcript variants encoding different isoforms. Additional splice variants have been described but their biological validity has not been confirmed.

Source: NCBI Gene 57082 — RefSeq curated summary.

At a glance

• Gene–disease (curated): microcephaly 4, primary, autosomal recessive (Strong, GenCC) — +1 more curated relationship
• GWAS associations: 10
• Clinical variants (ClinVar): 435 total — 5 pathogenic, 17 likely-pathogenic
• Phenotypes (HPO): 32
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 3 cancer types
• Cancer dependency (DepMap): dependent in 77.4% of screened cell lines
• MANE Select transcript: NM_144508

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24054
Approved symbol	KNL1
Name	kinetochore scaffold 1
Location	15q15.1
Locus type	gene with protein product
Status	Approved
Aliases	D40, AF15Q14, CT29, KIAA1570, hKNL-1, hSpc105, PPP1R55, Spc7
Ensembl gene	ENSG00000137812
Ensembl biotype	protein_coding
OMIM	609173
Entrez	57082

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000346991, ENST00000399668, ENST00000526913, ENST00000528967, ENST00000528975, ENST00000531626, ENST00000532056, ENST00000532347, ENST00000532406, ENST00000533001, ENST00000534204, ENST00000614337

RefSeq mRNA: 2 — MANE Select: NM_144508 NM_144508, NM_170589

CCDS: CCDS42023, CCDS42024

Canonical transcript exons

ENST00000399668 — 26 exons

Exon	Start	End
ENSE00000883907	40645656	40645772
ENSE00000930977	40628070	40628208
ENSE00000930979	40629273	40629371
ENSE00001312359	40646987	40647074
ENSE00001318594	40620640	40625640
ENSE00001321077	40628611	40628678
ENSE00001321397	40650301	40650378
ENSE00001539530	40659339	40659461
ENSE00001539531	40657355	40657473
ENSE00001539535	40657042	40657151
ENSE00003506724	40650544	40650583
ENSE00003508842	40606393	40606452
ENSE00003521653	40605110	40605149
ENSE00003533784	40618959	40619011
ENSE00003536596	40602915	40602966
ENSE00003584008	40615341	40615378
ENSE00003618303	40654909	40654977
ENSE00003630741	40640912	40641027
ENSE00003635527	40644997	40645087
ENSE00003659959	40611478	40611511
ENSE00003672499	40610245	40610297
ENSE00003682424	40608847	40608908
ENSE00003682477	40652005	40652105
ENSE00003685179	40651471	40651572
ENSE00003899568	40662074	40664342
ENSE00003901186	40594249	40594392

Expression profiles

Bgee: expression breadth ubiquitous, 193 present calls, max score 96.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.9483 / max 421.0361, expressed in 1396 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
146122	12.7326	1347
146121	0.7996	438
146123	0.3668	181
146124	0.0493	19

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	96.08	gold quality
ventricular zone	UBERON:0003053	92.90	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.96	gold quality
jejunal mucosa	UBERON:0000399	89.27	gold quality
secondary oocyte	CL:0000655	88.81	gold quality
sperm	CL:0000019	88.35	gold quality
ganglionic eminence	UBERON:0004023	86.43	gold quality
trabecular bone tissue	UBERON:0002483	86.07	gold quality
male germ cell	CL:0000015	85.07	gold quality
testis	UBERON:0000473	84.95	gold quality
oocyte	CL:0000023	84.75	gold quality
right testis	UBERON:0004534	84.04	gold quality
bone marrow	UBERON:0002371	83.05	gold quality
left testis	UBERON:0004533	83.00	gold quality
adult organism	UBERON:0007023	80.22	gold quality
duodenum	UBERON:0002114	79.85	gold quality
stromal cell of endometrium	CL:0002255	78.12	gold quality
bone marrow cell	CL:0002092	76.59	gold quality
adrenal tissue	UBERON:0018303	75.97	gold quality
lower esophagus mucosa	UBERON:0035834	74.39	gold quality
gingival epithelium	UBERON:0001949	73.72	silver quality
esophagus squamous epithelium	UBERON:0006920	72.99	gold quality
vermiform appendix	UBERON:0001154	72.14	gold quality
buccal mucosa cell	CL:0002336	72.01	silver quality
thymus	UBERON:0002370	71.86	gold quality
embryo	UBERON:0000922	71.85	gold quality
colonic epithelium	UBERON:0000397	71.75	gold quality
epithelium of nasopharynx	UBERON:0001951	71.22	gold quality
jejunum	UBERON:0002115	70.89	gold quality
tonsil	UBERON:0002372	70.67	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-3929	yes	7866.04
E-GEOD-75140	yes	887.42
E-GEOD-86618	yes	55.03
E-CURD-112	yes	36.92
E-MTAB-6678	yes	10.27
E-ANND-3	yes	6.02
E-CURD-10	no	132.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting KNL1, 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-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-150-3P	99.43	70.51	920
HSA-MIR-508-5P	99.41	64.25	1248
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-4686	98.77	66.87	964
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-500A-5P	98.76	69.13	1241
HSA-MIR-4725-5P	98.67	65.42	628
HSA-MIR-504-5P	98.67	65.40	631
HSA-MIR-3158-3P	98.45	64.25	560
HSA-MIR-3929	98.32	65.58	1026
HSA-MIR-6787-3P	97.75	66.17	1233
HSA-MIR-512-5P	97.47	66.48	591
HSA-MIR-4757-3P	88.86	63.55	51

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 32)

• a new cancer/testis gene frequently expressed in lung cancer of smokers (PMID:12087463)
• AF15q14 seems identical to an mRNA previously found to be expressed in melanoma rendered nontumorigenic by microcell-mediated introduction of normal chromosome 6, suggesting the gene may function normally to suppress cell growth and/or enhance maturation. (PMID:12618768)
• Blinkin may be the center of the network for generating kinetochore-based checkpoint signaling (PMID:17981135)
• the vertebrate KNL1 counterpart is essential for chromosome segregation and is required to localize a subset of outer kinetochore proteins. (PMID:18045986)
• c-Abl and D40 interact with the tumor suppressor pRb protein and subsequently can lead to regulation of the cell proliferation. (PMID:18771174)
• phosphorylation of KNL1 by Aurora B disrupts the KNL1-PP1 interaction (PMID:20231380)
• h-KNL1 functions to connect Bub1 and BubR1 with the hMis12, Ndc80, and Zwint-1 complexes. (PMID:21199919)
• Expression levels of D40 mRNA and proteins decrease according to the degree of spermatogenesis impairment in male infertile patients. (PMID:21272090)
• we identify the Blinkin motif critical for interaction with BUBR1, define the stoichiometry and affinity of the interaction, and present a 2.2 Angstrom resolution crystal structure of the complex (PMID:22000412)
• Data provide strong evidence for CASC5 as a novel MCPH gene, and underscore the role of kinetochore integrity in proper volumetric development of the human brain. (PMID:22983954)
• KNL1 contains an extensive array of short linear sequence modules that encompass TxxOmega and MELT motifs and that can independently localize BUB1. (PMID:24344183)
• KNL1 is a requirement for Aurora B activity at kinetochores and for wild-type kinetochore-MT attachment dynamics. (PMID:24344188)
• In cells depleted of endogenous Knl1, kinetochore-targeted Knl1(1-250) suffices to restore spindle assembly checkpoint and chromosome alignment (PMID:24361068)
• Protein phosphatase 1 (PP1) binding to KNL1 during prometaphase reduces the levels of Bub proteins at kinetochores to approximately the level recruited by four active MELT repeats. (PMID:24363448)
• PP2A-B56 is a key phosphatase for the removal of the Mps1-mediated Knl1 phosphorylations necessary for Bub1/BubR1 recruitment in mammalian cells. (PMID:25246613)
• Mechanisms of mitosis-specific assembly of the checkpoint platform Knl1/MIS12/NDC80 at human kinetochores. (PMID:25601404)
• Data show sequential multisite regulation of the microtubule-associated protein KNL1-kinase-adaptor complex BUB1/BUB3 interaction. (PMID:25661489)
• Targeted Knockdown of the Kinetochore Protein D40/Knl-1 Inhibits Human Cancer in a p53 Status-Independent Manner (PMID:26348410)
• We propose that CASC5 has a key role for the correct functioning of DNA damage response proteins, and a defect in this connection might affect upstream and downstream DNA damage response events as response to increased genotoxic stress. (PMID:26621532)
• Involvement of CASC5 in autosomal recessive microcephaly and a founder effect of the c.6125G>A mutation. (PMID:26626498)
• CASC5 may contribute to the morphological and structural changes of the human brain during recent evolution. The observed between-population divergence of CASC5 variants was driven by natural selection that tends to favor a larger gray matter volume in East Asians. (PMID:27878434)
• Therefore, Mps1 promotes checkpoint activation through sequentially phosphorylating Knl1, Bub1, and Mad1. This sequential multi-target phosphorylation cascade makes the checkpoint highly responsive to Mps1 and to kinetochore-microtubule attachment. (PMID:28072388)
• Mutations in the CASC5 gene were found to encode a kinetochore protein essential for mitotic cell division and to cause autosomal recessive primary microcephaly 4. (Review) (PMID:28901661)
• Data show how KNL1 binds both PP1 and microtubules. Unexpectedly, PP1 and microtubules bind KNL1 via overlapping binding sites. Co-sedimentation assays unequivocally demonstrated that microtubules and PP1 binding to KNL1 is mutually exclusive, with preferential formation of the KNL1:PP1 holoenzyme in the presence of PP1. (PMID:30100357)
• KNL1 mutation is associated with Microcephaly. (PMID:30304678)
• Study demonstrates that KNL1 acts as a receptor of linear ubiquitin chains to anchor CENP-E at attached kinetochores. Thus, linear ubiquitin chains constitute a critical mechanism for chromosome congression and alignment by coupling the dynamic kinetochore microtubule motor CENP-E to the static one, the KMN network. (PMID:30655516)
• KNL1 protein expression was also significantly associated with poorer survival. Moreover, there was a significant correlation between KNL1 and BUB1 in colorectal cancer tissues. KNL1 plays an effective role in decreasing apoptosis and promoting the proliferation of colorectal cancer cells, suggesting that its inhibition may represent a promising therapeutic approach in patients with colorectal cancer. (PMID:31315522)
• CASC5 is a potential tumour driving gene in lung adenocarcinoma. (PMID:32283571)
• LINC02418 promotes malignant behaviors in lung adenocarcinoma cells by sponging miR-4677-3p to upregulate KNL1 expression. (PMID:32795273)
• [CASC5 Gene Expression Changes Correlate with Targeted Mutations in Leukemia]. (PMID:33566033)
• A novel KNL1 intronic splicing variant likely destabilizes the KMN complex, causing primary microcephaly. (PMID:37937525)
• Kinetochore scaffold 1 downregulation suppressed the development of non-small cell lung cancer by inactivating the phosphatidylinositol 3 kinase/protein kinase B (AKT)/nuclear factor-kappa B pathway. (PMID:38583438)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	knl1	ENSDARG00000070239
mus_musculus	Knl1	ENSMUSG00000027326
rattus_norvegicus	Knl1	ENSRNOG00000060100

Protein

Protein identifiers

Outer kinetochore KNL1 complex subunit KNL1 — Q8NG31 (reviewed: Q8NG31)

Alternative names: ALL1-fused gene from chromosome 15q14 protein, Bub-linking kinetochore protein, Cancer susceptibility candidate gene 5 protein, Cancer/testis antigen 29, Kinetochore scaffold 1, Kinetochore-null protein 1, Protein CASC5, Protein D40/AF15q14

All UniProt accessions (6): A0A0G2JL96, A0A1Y8EIW7, Q8NG31, H0YCZ2, H0YEY7, H0YN41

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a component of the outer kinetochore KNL1 complex that serves as a docking point for spindle assembly checkpoint components and mediates microtubule-kinetochore interactions. Kinetochores, consisting of a centromere-associated inner segment and a microtubule-contacting outer segment, play a crucial role in chromosome segregation by mediating the physical connection between centromeric DNA and spindle microtubules. The outer kinetochore is made up of the ten-subunit KMN network, comprising the MIS12, NDC80 and KNL1 complexes, and auxiliary microtubule-associated components; together they connect the outer kinetochore with the inner kinetochore, bind microtubules, and mediate interactions with mitotic checkpoint proteins that delay anaphase until chromosomes are bioriented on the spindle. Required for kinetochore binding by a distinct subset of kMAPs (kinetochore-bound microtubule-associated proteins) and motors. Acts in coordination with CENPK to recruit the NDC80 complex to the outer kinetochore. Can bind either to microtubules or to the protein phosphatase 1 (PP1) catalytic subunits PPP1CA and PPP1CC (via overlapping binding sites), it has higher affinity for PP1. Recruits MAD2L1 to the kinetochore and also directly links BUB1 and BUB1B to the kinetochore. In addition to orienting mitotic chromosomes, it is also essential for alignment of homologous chromosomes during meiotic metaphase I. In meiosis I, required to activate the spindle assembly checkpoint at unattached kinetochores to correct erroneous kinetochore-microtubule attachments.

Subunit / interactions. Component of the KNL1 complex composed of KNL1 and ZWINT. Part of the ten-subunit outer kinetochore KMN network that includes the KNL1, MIS12 and NDC80 complexes; a bioriented kinetochore contains approximately 150 copies of the network. Interacts (via C-terminus) with the MIS12 complex subunits NSL1 (via C-terminus), PMF1 and DSN1; the interaction is direct. Interacts (via N-terminal region) with BUB1B (via BUB1 N-terminal domain); the interaction is direct and is required for cell cycle arrest upon activation of the mitotic spindle assembly checkpoint. Interacts (via N-terminal region) with BUB1 (via BUB1 N-terminal domain); the interaction is direct. Interacts with the protein phosphatase PP1 subunit PPP1CA; the interaction is direct and mutually exclusive with binding to microtubules. Interacts with the protein phosphatase PP1 subunit PPP1CC; the interaction is direct and mutually exclusive with binding to microtubules.

Subcellular location. Nucleus. Chromosome. Centromere. Kinetochore. Cytoplasm.

Tissue specificity. Highly expressed in testis, where it is localized in germ cells, in particular in spermatocytes and in the pre-acrosome of round spermatids. Detected in the acrosome of ejaculated spermatozoa. Detected in adult thymus, bone marrow, colon, small intestine, appendix and placenta, and in fetal liver and thymus.

Post-translational modifications. Phosphorylation by AURKB negatively regulates its interaction with protein phosphatase 1 (PP1) subunit PPP1CA and with microtubules.

Disease relevance. A chromosomal aberration involving KNL1 is associated with acute myeloblastic leukemia (AML). Translocation t(11;15)(q23;q14) with KMT2A. May give rise to a KMT2A-KNL1 fusion protein. Microcephaly 4, primary, autosomal recessive (MCPH4) [MIM:604321] A disease defined as a head circumference more than 3 standard deviations below the age-related mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. Despite this marked reduction in size, the gyral pattern is relatively well preserved, with no major abnormality in cortical architecture. Affected individuals have mild to moderate intellectual disability. Primary microcephaly is further defined by the absence of other syndromic features or significant neurological deficits due to degenerative brain disorder. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (4)

UniProt ID	Names	Canonical?
Q8NG31-1	1	yes
Q8NG31-2	2
Q8NG31-3	3
Q8NG31-4	4

RefSeq proteins (2): NP_653091, NP_733468 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037388	Blinkin	Family
IPR040850	Knl1_RWD_C	Domain
IPR043651	KNL1_MELT_rpt	Repeat

Pfam: PF18210, PF19221

UniProt features (93 total): modified residue 21, region of interest 13, sequence variant 13, helix 11, strand 9, turn 6, splice variant 5, sequence conflict 4, mutagenesis site 3, repeat 2, compositionally biased region 2, chain 1, coiled-coil region 1, short sequence motif 1, site 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
3SI5	X-RAY DIFFRACTION	2.2
4NFA	X-RAY DIFFRACTION	2.5
4A1G	X-RAY DIFFRACTION	2.6
4NF9	X-RAY DIFFRACTION	2.8
6CZO	X-RAY DIFFRACTION	2.95
8PPR	ELECTRON MICROSCOPY	3
8Q5H	ELECTRON MICROSCOPY	4.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NG31-F1	40.30	0.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 1818–1819 (breakpoint for translocation to form kmt2a-knl1)

Post-translational modifications (21): 24, 32, 60, 539, 578, 584, 586, 767, 901, 956, 1039, 1076, 1088, 1448, 1675, 1773, 1831, 1831, 1834, 1845 …

Mutagenesis-validated functional residues (3):

Position	Phenotype
24–25	decreases interaction with ppp1ca and abolishes binding to microtubules.
25–28	decreases interaction with ppp1ca.
60	decreases interaction with ppp1ca.

Function

Pathways and Gene Ontology

Reactome pathways

21 pathways

ID	Pathway
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-2467813	Separation of Sister Chromatids
R-HSA-2500257	Resolution of Sister Chromatid Cohesion
R-HSA-5663220	RHO GTPases Activate Formins
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-68877	Mitotic Prometaphase
R-HSA-9648025	EML4 and NUDC in mitotic spindle formation
R-HSA-141424	Amplification of signal from the kinetochores
R-HSA-162582	Signal Transduction
R-HSA-1640170	Cell Cycle
R-HSA-194315	Signaling by Rho GTPases
R-HSA-195258	RHO GTPase Effectors
R-HSA-2555396	Mitotic Metaphase and Anaphase
R-HSA-68882	Mitotic Anaphase
R-HSA-68886	M Phase
R-HSA-69278	Cell Cycle, Mitotic
R-HSA-69618	Mitotic Spindle Checkpoint
R-HSA-69620	Cell Cycle Checkpoints
R-HSA-73886	Chromosome Maintenance
R-HSA-774815	Nucleosome assembly
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 399 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_ATTACHMENT_OF_SPINDLE_MICROTUBULES_TO_KINETOCHORE, GOBP_REGULATION_OF_CELL_CYCLE_CHECKPOINT, GOBP_POSITIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, HORIUCHI_WTAP_TARGETS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GOBP_REGULATION_OF_MEIOTIC_NUCLEAR_DIVISION, GOBP_CHROMOSOME_LOCALIZATION, GOBP_CELL_CYCLE_PHASE_TRANSITION

GO Biological Process (9): mitotic sister chromatid segregation (GO:0000070), acrosome assembly (GO:0001675), attachment of spindle microtubules to kinetochore (GO:0008608), homologous chromosome orientation in meiotic metaphase I (GO:0031619), protein localization to kinetochore (GO:0034501), cell division (GO:0051301), regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266), positive regulation of meiosis I spindle assembly checkpoint (GO:1905326), chromosome segregation (GO:0007059)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (11): kinetochore (GO:0000776), outer kinetochore (GO:0000940), acrosomal vesicle (GO:0001669), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear body (GO:0016604), Knl1/Spc105 complex (GO:0180019), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Cell Cycle	3
Mitotic Prometaphase	2
M Phase	2
Amplification of signal from the kinetochores	1
Mitotic Anaphase	1
RHO GTPase Effectors	1
Nucleosome assembly	1
Mitotic Spindle Checkpoint	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Signaling by Rho GTPases	1
Mitotic Metaphase and Anaphase	1
Cell Cycle, Mitotic	1
Cell Cycle Checkpoints	1
Chromosome Maintenance	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	3
cellular anatomical structure	3
cell cycle process	2
protein-containing complex	2
sister chromatid segregation	1
mitotic nuclear division	1
mitotic cell cycle process	1
developmental process involved in reproduction	1
spermatid development	1
cellular component assembly involved in morphogenesis	1
cellular process involved in reproduction in multicellular organism	1
secretory granule organization	1
organelle assembly	1
microtubule binding	1
metaphase chromosome alignment	1
meiotic metaphase I homologous chromosome alignment	1
chromosome localization	1
protein localization to chromosome, centromeric region	1
protein localization to condensed chromosome	1
cellular process	1
regulation of mitotic nuclear division	1
mitotic spindle assembly checkpoint signaling	1
regulation of mitotic sister chromatid separation	1
regulation of mitotic metaphase/anaphase transition	1
regulation of mitotic sister chromatid segregation	1
regulation of mitotic spindle checkpoint	1
positive regulation of cell cycle process	1
positive regulation of spindle checkpoint	1
meiosis I spindle assembly checkpoint signaling	1
regulation of meiosis I spindle assembly checkpoint	1
positive regulation of reproductive process	1
tubulin binding	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
kinetochore	1
secretory granule	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

3072 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KNL1	BUB3	O43684	991
KNL1	ZWINT	O95229	986
KNL1	BUB1B	O60566	985
KNL1	MIS12	Q9H081	973
KNL1	BUB1	O43683	972
KNL1	DSN1	Q9H410	948
KNL1	NDC80	O14777	937
KNL1	AURKB	Q96GD4	882
KNL1	SPC24	Q8NBT2	837
KNL1	NSL1	Q96IY1	827
KNL1	NUF2	Q9BZD4	823
KNL1	CENPE	Q02224	821
KNL1	A0A087WT04	A0A087WT04	819
KNL1	PMF1	Q6P1K2	814
KNL1	PPP1CC	P36873	789

IntAct

137 interactions, top by confidence:

A	B	Type	Score
NUF2	NDC80	psi-mi:“MI:0914”(association)	0.950
ZWINT	NDC80	psi-mi:“MI:0914”(association)	0.940
SPC25	NDC80	psi-mi:“MI:0914”(association)	0.940
BUB1B	BUB3	psi-mi:“MI:0914”(association)	0.930
SPC24	NDC80	psi-mi:“MI:0914”(association)	0.920
DSN1	ZWINT	psi-mi:“MI:0914”(association)	0.900
MIS12	ZWINT	psi-mi:“MI:0914”(association)	0.900
MIS12	NDC80	psi-mi:“MI:0914”(association)	0.850
DSN1	KNL1	psi-mi:“MI:0914”(association)	0.840
DSN1	NDC80	psi-mi:“MI:0914”(association)	0.790
RFXANK	RFXAP	psi-mi:“MI:0914”(association)	0.780
KNL1	SPC24	psi-mi:“MI:0914”(association)	0.760
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
BUB1	KNL1	psi-mi:“MI:0915”(physical association)	0.690
KNL1	PPP1CA	psi-mi:“MI:0407”(direct interaction)	0.690
BUB3	ZNF207	psi-mi:“MI:0914”(association)	0.690
KNL1	PPP1CA	psi-mi:“MI:0915”(physical association)	0.690
KNL1	PPP1CC	psi-mi:“MI:0407”(direct interaction)	0.690
BUB1	NDC80	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (229): CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Affinity Capture-MS), CASC5 (Synthetic Lethality), CASC5 (Proximity Label-MS), CASC5 (Proximity Label-MS), CD97 (Affinity Capture-MS)

ESM2 similar proteins: A2RRX6, A4IFU8, A5D7U0, A5PK21, A6QNQ6, B0BM16, B1H1S4, B1WC58, O43303, P16128, P51816, Q08DI1, Q14207, Q15398, Q28FY7, Q2M2Z5, Q32PP1, Q3UHX0, Q49A88, Q569L8, Q5BQN8, Q5FBB7, Q5HZI1, Q5QGS0, Q5R9I1, Q5RD97, Q5SVT3, Q5W0B1, Q6GNV6, Q6NZG4, Q6P0N0, Q6PDM4, Q6ZU52, Q7SZL5, Q7ZZH7, Q80WQ8, Q80YR6, Q86WS4, Q8CDD9, Q8IYA6

Diamond homologs: Q66JQ7, Q8NG31

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
KNL1	up-regulates	BUB1	binding
KNL1	up-regulates	BUB1B	binding
AURKB	down-regulates	KNL1	phosphorylation
KNL1	“form complex”	“KNL1 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 141 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:

Pathway	Partners	Fold	FDR
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	12	15.5×	2e-09
Amplification of signal from the kinetochores	7	15.3×	2e-05
Resolution of Sister Chromatid Cohesion	14	13.5×	1e-09
EML4 and NUDC in mitotic spindle formation	13	13.4×	2e-09
Mitotic Spindle Checkpoint	7	12.3×	6e-05
RHO GTPases Activate Formins	14	12.1×	2e-09
mRNA 3’-end processing	5	10.9×	2e-03
Cell Cycle Checkpoints	11	10.8×	4e-07

GO biological processes:

GO term	Partners	Fold	FDR
attachment of spindle microtubules to kinetochore	9	68.5×	2e-12
mitotic spindle assembly checkpoint signaling	9	41.1×	3e-10
mitotic sister chromatid segregation	6	23.5×	4e-05
chromosome segregation	7	9.9×	1e-03
cell division	18	6.8×	5e-08
mRNA splicing, via spliceosome	8	6.0×	8e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 3 cancer types — BCC, GBM, HCC.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	17
Uncertain significance	185
Likely benign	101
Benign	51

Top pathogenic / likely-pathogenic (22)

Variant ID	HGVS	Classification
1220018	NM_144508.5(KNL1):c.1810C>T (p.Gln604Ter)	Pathogenic
1690305	NM_144508.5(KNL1):c.1076del (p.Gly359fs)	Pathogenic
217515	NM_144508.5(KNL1):c.5184dup (p.Ile1729fs)	Pathogenic
2273066	NM_144508.5(KNL1):c.4693_4696del (p.Asn1565fs)	Pathogenic
39707	NM_144508.5(KNL1):c.6045G>A (p.Met2015Ile)	Pathogenic
1201481	NM_144508.5(KNL1):c.3579del (p.Gly1194fs)	Likely pathogenic
1204492	NM_144508.5(KNL1):c.6872C>T (p.Pro2291Leu)	Likely pathogenic
1684287	NM_144508.5(KNL1):c.2044_2047del (p.Lys681_Gln682insTer)	Likely pathogenic
210578	NM_144508.5(KNL1):c.694del (p.Asp232fs)	Likely pathogenic
2441015	NM_144508.5(KNL1):c.197_197+4del	Likely pathogenic
3337238	NM_144508.5(KNL1):c.4537del (p.Thr1513fs)	Likely pathogenic
3357745	NM_144508.5(KNL1):c.6172+2T>C	Likely pathogenic
3779800	NM_144508.5(KNL1):c.4076_4077del (p.Ser1359fs)	Likely pathogenic
422642	NM_144508.5(KNL1):c.5542_5543del (p.Gln1848fs)	Likely pathogenic
423391	NM_144508.5(KNL1):c.6304del (p.Asp2102fs)	Likely pathogenic
434584	NM_144508.5(KNL1):c.4745_4746delinsC (p.Leu1582fs)	Likely pathogenic
445348	NM_144508.5(KNL1):c.5130dup (p.Ile1711fs)	Likely pathogenic
489319	NM_144508.5(KNL1):c.5542C>T (p.Gln1848Ter)	Likely pathogenic
495234	NM_144508.5(KNL1):c.6349G>T (p.Asp2117Tyr)	Likely pathogenic
495235	NM_144508.5(KNL1):c.1521A>G (p.Gln507=)	Likely pathogenic
817148	NM_144508.5(KNL1):c.424_427del (p.Thr142fs)	Likely pathogenic
817944	NM_144508.5(KNL1):c.6125del (p.Asn2042fs)	Likely pathogenic

SpliceAI

3489 predictions. Top by Δscore:

Variant	Effect	Δscore
15:40602914:GAAAA:G	acceptor_gain	1.0000
15:40602962:GAAAA:G	donor_gain	1.0000
15:40602967:G:GG	donor_gain	1.0000
15:40605150:G:GG	donor_gain	1.0000
15:40608909:G:GG	donor_gain	1.0000
15:40610241:CTAG:C	acceptor_loss	1.0000
15:40610242:TA:T	acceptor_loss	1.0000
15:40610243:A:AG	acceptor_gain	1.0000
15:40610243:AG:A	acceptor_gain	1.0000
15:40610243:AGG:A	acceptor_gain	1.0000
15:40610244:G:A	acceptor_gain	1.0000
15:40610244:G:GC	acceptor_gain	1.0000
15:40610244:GGG:G	acceptor_gain	1.0000
15:40610244:GGGT:G	acceptor_gain	1.0000
15:40610244:GGGTA:G	acceptor_gain	1.0000
15:40610293:GGAAG:G	donor_gain	1.0000
15:40610294:GAAG:G	donor_gain	1.0000
15:40610294:GAAGG:G	donor_gain	1.0000
15:40610295:AAG:A	donor_gain	1.0000
15:40610295:AAGG:A	donor_loss	1.0000
15:40610296:AG:A	donor_gain	1.0000
15:40610297:GG:G	donor_gain	1.0000
15:40610298:G:GA	donor_loss	1.0000
15:40610298:G:GG	donor_gain	1.0000
15:40619009:G:GT	donor_gain	1.0000
15:40628206:GCA:G	donor_gain	1.0000
15:40628209:G:GG	donor_gain	1.0000
15:40628226:GC:G	donor_gain	1.0000
15:40628227:C:G	donor_gain	1.0000
15:40629367:GCAAT:G	donor_gain	1.0000

AlphaMissense

15630 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:40608892:T:C	F61L	0.995
15:40608894:T:A	F61L	0.995
15:40608894:T:G	F61L	0.995
15:40652015:T:A	W2135R	0.995
15:40652015:T:C	W2135R	0.995
15:40652079:T:C	L2156P	0.995
15:40652052:T:C	F2147S	0.992
15:40659347:T:C	L2267P	0.991
15:40659353:T:C	F2269S	0.990
15:40659379:T:C	F2278L	0.988
15:40659381:T:A	F2278L	0.988
15:40659381:T:G	F2278L	0.988
15:40662139:T:A	V2327D	0.988
15:40657081:T:C	L2201P	0.987
15:40608893:T:C	F61S	0.986
15:40652057:T:C	F2149L	0.986
15:40652059:T:A	F2149L	0.986
15:40652059:T:G	F2149L	0.986
15:40608889:A:C	S60R	0.985
15:40608891:C:A	S60R	0.985
15:40608891:C:G	S60R	0.985
15:40606401:A:C	K28N	0.984
15:40606401:A:T	K28N	0.984
15:40652045:G:C	A2145P	0.984
15:40652017:G:C	W2135C	0.983
15:40652017:G:T	W2135C	0.983
15:40659352:T:C	F2269L	0.983
15:40659354:C:A	F2269L	0.983
15:40659354:C:G	F2269L	0.983
15:40606397:T:C	L27S	0.982

dbSNP variants (sampled 300 via entrez): RS1000000937 (15:40651450 A>G), RS1000043102 (15:40614652 C>G,T), RS1000062764 (15:40640122 A>G,T), RS1000070190 (15:40614096 C>A), RS1000144166 (15:40664677 T>C), RS1000154424 (15:40630147 A>G), RS1000228923 (15:40657662 C>T), RS1000312423 (15:40617189 T>A), RS1000484793 (15:40628305 G>A), RS1000521893 (15:40596915 A>C), RS1000569848 (15:40604861 A>C), RS1000577719 (15:40646375 A>G), RS1000634838 (15:40611097 A>T), RS1000660583 (15:40634702 A>G), RS1000669949 (15:40640813 A>G)

Disease associations

OMIM: gene MIM:609173 | disease phenotypes: MIM:604321

GenCC curated gene-disease

Disease	Classification	Inheritance
microcephaly 4, primary, autosomal recessive	Strong	Autosomal recessive
autosomal recessive primary microcephaly	Supportive	Autosomal recessive

Mondo (2): microcephaly 4, primary, autosomal recessive (MONDO:0011437), autosomal recessive primary microcephaly (MONDO:0016660)

Orphanet (1): Autosomal recessive primary microcephaly (Orphanet:2512)

HPO phenotypes

32 total (30 of 32 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000076	Vesicoureteral reflux
HP:0000122	Unilateral renal agenesis
HP:0000219	Thin upper lip vermilion
HP:0000252	Microcephaly
HP:0000316	Hypertelorism
HP:0000340	Sloping forehead
HP:0000347	Micrognathia
HP:0000574	Thick eyebrow
HP:0000582	Upslanted palpebral fissure
HP:0000664	Synophrys
HP:0000718	Aggressive behavior
HP:0000750	Delayed speech and language development
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001263	Global developmental delay
HP:0001274	Agenesis of corpus callosum
HP:0001302	Pachygyria
HP:0001320	Cerebellar vermis hypoplasia
HP:0001335	Bimanual synkinesia
HP:0001347	Hyperreflexia
HP:0001510	Growth delay
HP:0002119	Ventriculomegaly
HP:0002282	Gray matter heterotopia
HP:0003103	Abnormal cortical bone morphology
HP:0003577	Congenital onset
HP:0004322	Short stature
HP:0007333	Hypoplasia of the frontal lobes
HP:0009765	Low hanging columella
HP:0010864	Severe intellectual disability

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST006085_61	Prostate cancer	1.000000e-08
GCST008559_8	Anxiety and stress-related disorders	7.000000e-07
GCST010002_167	Refractive error	3.000000e-11
GCST010725_23	Malaria	2.000000e-06
GCST010725_38	Malaria	3.000000e-06
GCST010725_80	Malaria	7.000000e-06
GCST011320_29	Type 2 diabetes or prostate cancer (pleiotropy)	3.000000e-09
GCST90002388_145	Lymphocyte count	3.000000e-13
GCST90020025_443	Waist-to-hip ratio adjusted for BMI	3.000000e-09
GCST90020027_621	Waist-hip index	6.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0010098	stress-related disorder
EFO:0004587	lymphocyte count
EFO:0007788	BMI-adjusted waist-hip ratio

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C579935	Autosomal Recessive Primary Microcephaly (supp.)
C565792	Microcephaly, Primary Autosomal Recessive, 4 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	5
Valproic Acid	affects expression, decreases expression, decreases methylation	5
bisphenol A	decreases expression, affects cotreatment	2
trichostatin A	affects cotreatment, decreases expression	2
perfluoro-n-nonanoic acid	decreases expression	2
Arsenic	increases expression, affects cotreatment, decreases expression, increases abundance	2
Doxorubicin	decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
geldanamycin	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	decreases expression	1
3,4-dichloroaniline	decreases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	increases expression	1
diallyl trisulfide	decreases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
deguelin	increases expression	1
fenpyroximate	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1

Clinical trials (associated diseases)

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