SKA3

Summary

SKA3 (spindle and kinetochore associated complex subunit 3, HGNC:20262) is a protein-coding gene on chromosome 13q12.11, encoding Spindle and kinetochore-associated protein 3 (Q8IX90). Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation. It is a selective cancer dependency (DepMap: 77.4% of cell lines).

This gene encodes a component of the spindle and kinetochore-associated protein complex that regulates microtubule attachment to the kinetochores during mitosis. The encoded protein localizes to the outer kinetechore and may be required for normal chromosome segregation and cell division. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 221150 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 78 total
• Cancer dependency (DepMap): dependent in 77.4% of screened cell lines
• MANE Select transcript: NM_145061

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20262
Approved symbol	SKA3
Name	spindle and kinetochore associated complex subunit 3
Location	13q12.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC4832, RAMA1
Ensembl gene	ENSG00000165480
Ensembl biotype	protein_coding
OMIM	619247
Entrez	221150

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron

ENST00000298260, ENST00000314759, ENST00000400018, ENST00000462482, ENST00000465471, ENST00000475251, ENST00000536239, ENST00000894558, ENST00000921404, ENST00000921405, ENST00000921406, ENST00000921407, ENST00000921408, ENST00000921409

RefSeq mRNA: 2 — MANE Select: NM_145061 NM_001166017, NM_145061

CCDS: CCDS31946, CCDS53856

Canonical transcript exons

ENST00000314759 — 9 exons

Exon	Start	End
ENSE00001093509	21176375	21176552
ENSE00003463391	21161790	21161875
ENSE00003499323	21172620	21172681
ENSE00003564150	21157922	21158125
ENSE00003592340	21153595	21155150
ENSE00003625350	21167988	21168399
ENSE00003657945	21159902	21159987
ENSE00003659547	21155693	21155811
ENSE00003668602	21172339	21172504

Expression profiles

Bgee: expression breadth ubiquitous, 152 present calls, max score 89.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.7430 / max 332.3969, expressed in 1334 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136384	12.7430	1334

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	89.77	gold quality
secondary oocyte	CL:0000655	88.34	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.09	gold quality
oocyte	CL:0000023	86.70	gold quality
embryo	UBERON:0000922	85.95	gold quality
ganglionic eminence	UBERON:0004023	85.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.05	gold quality
ileal mucosa	UBERON:0000331	82.07	gold quality
sperm	CL:0000019	78.17	silver quality
stromal cell of endometrium	CL:0002255	75.38	gold quality
right testis	UBERON:0004534	75.14	gold quality
mucosa of transverse colon	UBERON:0004991	75.05	gold quality
pancreatic ductal cell	CL:0002079	74.89	silver quality
bone marrow cell	CL:0002092	73.63	gold quality
testis	UBERON:0000473	73.46	gold quality
left testis	UBERON:0004533	73.44	gold quality
bone marrow	UBERON:0002371	73.30	gold quality
rectum	UBERON:0001052	72.76	gold quality
amniotic fluid	UBERON:0000173	72.37	silver quality
esophagus squamous epithelium	UBERON:0006920	70.80	silver quality
vermiform appendix	UBERON:0001154	70.63	gold quality
adrenal tissue	UBERON:0018303	70.32	gold quality
lower esophagus mucosa	UBERON:0035834	70.20	gold quality
esophagus mucosa	UBERON:0002469	70.13	gold quality
tibialis anterior	UBERON:0001385	68.50	silver quality
smooth muscle tissue	UBERON:0001135	67.39	gold quality
tibia	UBERON:0000979	66.83	silver quality
lymph node	UBERON:0000029	66.69	gold quality
gingival epithelium	UBERON:0001949	66.58	gold quality
duodenum	UBERON:0002114	66.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.78
E-GEOD-99795	no	222.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting SKA3, 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-12136	99.98	72.81	5713
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-217-5P	99.49	69.93	1419
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-133A-3P	99.27	71.53	1270
HSA-MIR-133B	99.27	71.53	1270
HSA-MIR-505-3P	99.19	69.71	896

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 29)

• C13Orf3 (now termed Ska3) localizes to the spindle and kinetochore throughout mitosis and its depletion markedly delays anaphase transition. (PMID:19360002)
• These data identify C13orf3 (Ska3) as an important factor for metaphase to anaphase progression and highlight the potential of combined RNAi screening and protein localisation analyses. (PMID:19387489)
• RAMA1 is a novel kinetochore protein involved in kinetochore-microtubule attachment. (PMID:19549680)
• Ska3 functions to coordinate checkpoint signaling from the microtubule binding sites within a kinetochore by laterally linking the individual binding sites. (PMID:19646878)
• Data suggest that Aurora B phosphorylation antagonizes the interaction between the Ska1-3 complex and the KMN network, thereby controlling Ska recruitment to KTs and stabilization of KT-MT attachments. (PMID:22371557)
• The structure of the Ska core complex is a W-shaped dimer of coiled coils, formed by intertwined interactions between Ska1, Ska2, and Ska3. (PMID:22483620)
• over-expression of GNL3 and SKA3 in the PC-3 human prostate cancer cell line decreased in vitro cell migration and invasion (PMID:26429724)
• 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)
• Study shows that Cdk1 phosphorylates Ska3 to promote its direct binding to the Ndc80 complex (Ndc80C), a core outer kinetochore component, also show that this phosphorylation occurs specifically during mitosis and is required for the kinetochore localization of the Ska complex. (PMID:28479321)
• Kinetochores mature through Ska1/ska2/Ska3 complex recruitment and this is required for improved load-bearing capacity and silencing of the spindle assembly checkpoint. (PMID:28495837)
• decreased neuronal cell SKA complex genes’ expression levels affect neuronal cell viability and neurite development (PMID:29268205)
• SKA3 Promotes tumor growth by regulating CDK2/P53 phosphorylation in hepatocellular carcinoma. (PMID:31804459)
• SKA3 promotes lung adenocarcinoma metastasis through the EGFR-PI3K-Akt axis. (PMID:32068236)
• The Circular RNA circSKA3 Binds Integrin beta1 to Induce Invadopodium Formation Enhancing Breast Cancer Invasion. (PMID:32229309)
• Multisite phosphorylation determines the formation of Ska-Ndc80 macro-complexes that are essential for chromosome segregation during mitosis. (PMID:32491969)
• SKA3 Promotes Cell Growth in Breast Cancer by Inhibiting PLK-1 Protein Degradation. (PMID:32799774)
• Targeting SKA3 suppresses the proliferation and chemoresistance of laryngeal squamous cell carcinoma via impairing PLK1-AKT axis-mediated glycolysis. (PMID:33106477)
• Spindle and kinetochoreassociated complex subunit 3 accelerates breast cancer cell proliferation and invasion through the regulation of Akt/Wnt/beta-catenin signaling. (PMID:33423159)
• Upregulation of SKA3 enhances cell proliferation and correlates with poor prognosis in hepatocellular carcinoma. (PMID:33760206)
• Circ-SKA3 upregulates ID3 expression by decoying miR-326 to accelerate the development of medulloblastoma. (PMID:33775353)
• SKA3 promotes glioblastoma proliferation and invasion by enhancing the activation of Wnt/beta-catenin signaling via modulation of the Akt/GSK-3beta axis. (PMID:33895155)
• Transcript levels of spindle and kinetochore-associated complex 1/3 as prognostic biomarkers correlated with immune infiltrates in hepatocellular carcinoma. (PMID:34045512)
• Circ-SKA3 Enhances Doxorubicin Toxicity in AC16 Cells Through miR-1303/TLR4 Axis. (PMID:34544967)
• MiR-133b suppresses the proliferation, migration and invasion of lung adenocarcinoma cells by targeting SKA3. (PMID:34711122)
• SKA3 is a prognostic biomarker and associated with immune infiltration in bladder cancer. (PMID:35546682)
• Transcription factor ZEB1 regulates PLK1-mediated SKA3 phosphorylation to promote lung cancer cell proliferation, migration and cell cycle. (PMID:36728910)
• Hypoxia-induced SKA3 promoted cholangiocarcinoma progression and chemoresistance by enhancing fatty acid synthesis via the regulation of PAR-dependent HIF-1a deubiquitylation. (PMID:37821935)
• Specific intracellular retention of circSKA3 promotes colorectal cancer metastasis by attenuating ubiquitination and degradation of SLUG. (PMID:37973787)
• Spindle and kinetochore-related complex subunit 3 has a protumour function in osteosarcoma by activating the Notch pathway. (PMID:38228236)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ska3	ENSDARG00000069917
mus_musculus	Ska3	ENSMUSG00000021965
rattus_norvegicus	Ska3	ENSRNOG00000021847

Protein

Protein identifiers

Spindle and kinetochore-associated protein 3 — Q8IX90 (reviewed: Q8IX90)

All UniProt accessions (3): Q8IX90, F5GWG1, F5H8H7

UniProt curated annotations — full annotation on UniProt →

Function. Component of the SKA1 complex, a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation. The SKA1 complex is a direct component of the kinetochore-microtubule interface and directly associates with microtubules as oligomeric assemblies. The complex facilitates the processive movement of microspheres along a microtubule in a depolymerization-coupled manner. In the complex, it mediates the microtubule-stimulated oligomerization. Affinity for microtubules is synergistically enhanced in the presence of the ndc-80 complex and may allow the ndc-80 complex to track depolymerizing microtubules.

Subunit / interactions. Component of the SKA1 complex, composed of SKA1, SKA2 and SKA3. The core SKA1 complex is composed of 2 SKA1-SKA2 heterodimers, each heterodimer interacting with a molecule of the SKA3 homodimer. The core SKA1 complex associates with microtubules and forms oligomeric assemblies. Interacts with SKA1; the interaction is direct.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle. Chromosome. Centromere. Kinetochore.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the SKA3 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8IX90-1	1	yes
Q8IX90-2	2
Q8IX90-3	3

RefSeq proteins (2): NP_001159489, NP_659498* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR033341	SKA3	Family

UniProt features (22 total): modified residue 10, splice variant 3, sequence variant 3, helix 3, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4AJ5	X-RAY DIFFRACTION	3.32

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IX90-F1	64.35	0.25

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 (10): 267, 318, 384, 34, 119, 139, 152, 155, 159, 265

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 254 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, GOBP_ESTABLISHMENT_OF_SPINDLE_ORIENTATION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_NUCLEAR_DIVISION, GOBP_ATTACHMENT_OF_SPINDLE_MICROTUBULES_TO_KINETOCHORE, GOBP_REGULATION_OF_CELL_CYCLE_CHECKPOINT, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, HORIUCHI_WTAP_TARGETS_DN, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_REGULATION_OF_NUCLEAR_DIVISION, GOBP_SPINDLE_LOCALIZATION, GOBP_CHROMOSOME_LOCALIZATION, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_POSITIVE_REGULATION_OF_MITOTIC_CELL_CYCLE

GO Biological Process (11): mitotic sister chromatid segregation (GO:0000070), mitotic cell cycle (GO:0000278), spindle assembly involved in female meiosis (GO:0007056), chromosome segregation (GO:0007059), mitotic metaphase chromosome alignment (GO:0007080), regulation of microtubule polymerization or depolymerization (GO:0031110), establishment of meiotic spindle orientation (GO:0051296), cell division (GO:0051301), metaphase chromosome alignment (GO:0051310), attachment of mitotic spindle microtubules to kinetochore (GO:0051315), negative regulation of mitotic spindle assembly checkpoint signaling (GO:0140499)

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

GO Cellular Component (14): kinetochore (GO:0000776), outer kinetochore (GO:0000940), centrosome (GO:0005813), cytosol (GO:0005829), spindle microtubule (GO:0005876), mitotic spindle (GO:0072686), meiotic spindle (GO:0072687), SKA complex (GO:0170027), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoplasm (GO:0005737), spindle (GO:0005819), cytoskeleton (GO:0005856), microtubule (GO:0005874)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	4
mitotic cell cycle process	3
spindle	3
mitotic nuclear division	2
protein-containing complex	2
cellular anatomical structure	2
microtubule cytoskeleton	2
sister chromatid segregation	1
cell cycle	1
female meiotic nuclear division	1
meiotic spindle assembly	1
cell cycle process	1
mitotic sister chromatid segregation	1
mitotic cell cycle	1
metaphase chromosome alignment	1
microtubule polymerization or depolymerization	1
regulation of microtubule cytoskeleton organization	1
establishment of spindle orientation	1
establishment of meiotic spindle localization	1
meiotic cell cycle	1
cellular process	1
chromosome localization	1
nuclear chromosome segregation	1
mitotic metaphase chromosome alignment	1
attachment of spindle microtubules to kinetochore	1
mitotic spindle assembly checkpoint signaling	1
negative regulation of cell cycle process	1
positive regulation of mitotic metaphase/anaphase transition	1
positive regulation of mitotic sister chromatid segregation	1
negative regulation of spindle checkpoint	1
regulation of mitotic cell cycle spindle assembly checkpoint	1
tubulin binding	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
kinetochore	1
centriole	1
microtubule organizing center	1
cytoplasm	1
microtubule	1

Protein interactions and networks

STRING

1476 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SKA3	SKA2	Q8WVK7	996
SKA3	SKA1	Q96BD8	995
SKA3	KNL1	Q8NG31	714
SKA3	NUF2	Q9BZD4	713
SKA3	CENPE	Q02224	679
SKA3	HMMR	O75330	642
SKA3	NDC80	O14777	629
SKA3	TPX2	Q9ULW0	576
SKA3	SPC24	Q8NBT2	572
SKA3	CENPN	Q96H22	563
SKA3	CCNA2	P20248	559
SKA3	HAUS6	Q7Z4H7	544
SKA3	CENPO	Q9BU64	542
SKA3	DSN1	Q9H410	538
SKA3	SPC25	Q9HBM1	515

IntAct

68 interactions, top by confidence:

A	B	Type	Score
SKA1	SKA3	psi-mi:“MI:0915”(physical association)	0.930
SKA3	SKA1	psi-mi:“MI:0915”(physical association)	0.930
SKA3	SKA1	psi-mi:“MI:0403”(colocalization)	0.930
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
SKA2	SKA3	psi-mi:“MI:0914”(association)	0.830
SKA3	SKA2	psi-mi:“MI:0914”(association)	0.830
PPP2R2D	YEATS4	psi-mi:“MI:0914”(association)	0.730
PPP2R2C	PPP2R1A	psi-mi:“MI:0914”(association)	0.730
PPP2R2B	MYO9A	psi-mi:“MI:0914”(association)	0.640
PPP2R2C	TCP1	psi-mi:“MI:0914”(association)	0.640
SKA3	NOL4	psi-mi:“MI:0914”(association)	0.640
NOL4	SKA3	psi-mi:“MI:0915”(physical association)	0.560
CEP104	CCDC66	psi-mi:“MI:2364”(proximity)	0.540
SKA3	CCDC85C	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
KIAA0753	OFD1	psi-mi:“MI:2364”(proximity)	0.480
SKA3	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
PPP2R2B	TCP1	psi-mi:“MI:0914”(association)	0.420
PPP2R2B	TCP1	psi-mi:“MI:2364”(proximity)	0.420
ZDHHC17	SKA3	psi-mi:“MI:0915”(physical association)	0.370
SKA1	ILVBL	psi-mi:“MI:0914”(association)	0.350
Ska1	HSPD1	psi-mi:“MI:0914”(association)	0.350
SKA3	RTL8C	psi-mi:“MI:0914”(association)	0.350
SKA3	AP3B1	psi-mi:“MI:0914”(association)	0.350

BioGRID (234): SKA3 (Two-hybrid), SKA3 (Affinity Capture-MS), SKA3 (Affinity Capture-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), SKA3 (Proximity Label-MS), ECT2 (Affinity Capture-MS), GDI2 (Affinity Capture-MS), KRT3 (Affinity Capture-MS), MYO5B (Affinity Capture-MS)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A2AHC3, A2AIW0, A5D8S0, A5WUN7, A8PUI7, B0BM16, B1H1S4, B2GUZ2, B7ZS37, D3IUT5, D3Z8E6, D4AEC2, F1QB81, F1R983, P53995, Q08AD1, Q0VF22, Q13129, Q16533, Q2KHM9, Q2T9I9, Q49A88, Q4R815, Q58EL7, Q5CZC0, Q5RHB5, Q5T5Y3, Q66H35, Q6DJL7, Q6DRL4, Q6IRN6, Q6PUR7, Q7L2Z9, Q7Z4H7, Q8C263, Q8CGZ2, Q8CJ27

Diamond homologs: A8PUI7, B0BM16, B1H1S4, B2GUZ2, Q58EL7, Q8C263, Q8IX90

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
CDK1	“up-regulates activity”	SKA3	phosphorylation
AURKB	“up-regulates activity”	SKA3	phosphorylation
SKA3	“form complex”	“SKA complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 70 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
Cell Cycle Checkpoints	7	15.5×	4e-05
RHO GTPase Effectors	7	11.9×	2e-04
M Phase	6	9.9×	1e-03
RHO GTPases Activate Formins	5	9.7×	3e-03
Mitotic Prometaphase	5	8.7×	4e-03
Signaling by Rho GTPases	10	8.6×	4e-05
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	10	8.4×	4e-05
Cell Cycle, Mitotic	6	7.2×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1410 predictions. Top by Δscore:

Variant	Effect	Δscore
13:21155151:C:CC	acceptor_gain	1.0000
13:21155689:TCAC:T	donor_loss	1.0000
13:21155692:C:A	donor_loss	1.0000
13:21155807:AAAAG:A	acceptor_gain	1.0000
13:21155808:AAAG:A	acceptor_gain	1.0000
13:21155809:AAG:A	acceptor_gain	1.0000
13:21155810:AG:A	acceptor_gain	1.0000
13:21155811:GC:G	acceptor_loss	1.0000
13:21155812:C:CA	acceptor_loss	1.0000
13:21155812:C:CC	acceptor_gain	1.0000
13:21155813:T:A	acceptor_loss	1.0000
13:21157953:T:TA	donor_gain	1.0000
13:21161887:C:CT	acceptor_gain	1.0000
13:21161888:A:AC	acceptor_gain	1.0000
13:21161897:T:TC	acceptor_gain	1.0000
13:21168180:T:TA	donor_gain	1.0000
13:21168397:GTACT:G	acceptor_loss	1.0000
13:21168399:ACTAG:A	acceptor_loss	1.0000
13:21168400:C:CC	acceptor_gain	1.0000
13:21168400:CTA:C	acceptor_loss	1.0000
13:21172689:A:C	acceptor_gain	1.0000
13:21172696:T:C	acceptor_gain	1.0000
13:21172696:T:TC	acceptor_gain	1.0000
13:21172719:A:AC	acceptor_gain	1.0000
13:21172719:A:C	acceptor_gain	1.0000
13:21176373:A:AC	donor_gain	1.0000
13:21176374:C:CC	donor_gain	1.0000
13:21176374:CCG:C	donor_gain	1.0000
13:21176380:T:A	donor_gain	1.0000
13:21155148:TTT:T	acceptor_gain	0.9900

AlphaMissense

2718 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:21168248:A:C	F161L	0.990
13:21168248:A:T	F161L	0.990
13:21168250:A:G	F161L	0.990
13:21168243:A:G	L163P	0.977
13:21168249:A:G	F161S	0.975
13:21168243:A:T	L163H	0.973
13:21176404:A:G	L25P	0.964
13:21172645:A:G	L47P	0.961
13:21176446:A:G	L11P	0.953
13:21168258:A:T	L158H	0.949
13:21168246:C:T	G162E	0.948
13:21168243:A:C	L163R	0.946
13:21168266:A:C	S155R	0.943
13:21168266:A:T	S155R	0.943
13:21168268:T:G	S155R	0.943
13:21176425:A:G	L18P	0.943
13:21168246:C:A	G162V	0.940
13:21168249:A:C	F161C	0.940
13:21172425:A:G	L82P	0.935
13:21168264:G:T	P156Q	0.934
13:21168252:T:C	D160G	0.924
13:21168062:A:C	F223L	0.921
13:21168062:A:T	F223L	0.921
13:21168064:A:G	F223L	0.921
13:21172620:C:A	K55N	0.920
13:21172620:C:G	K55N	0.920
13:21168265:G:A	P156S	0.919
13:21172624:A:G	L54P	0.919
13:21176437:A:G	L14P	0.918
13:21168247:C:G	G162R	0.917

dbSNP variants (sampled 300 via entrez): RS1000055454 (13:21174738 A>T), RS1000202391 (13:21155000 A>G), RS1000254243 (13:21160751 C>A), RS1000368981 (13:21167813 A>T), RS1000426098 (13:21173776 A>C), RS1000524571 (13:21159967 G>A), RS1000536168 (13:21160420 A>G), RS1000584247 (13:21166500 G>A,C), RS1000635410 (13:21165333 G>A), RS1000835557 (13:21177917 C>T), RS1001108435 (13:21177333 C>G,T), RS1001177455 (13:21153763 C>A,T), RS1001287785 (13:21177699 G>A), RS1001293705 (13:21153388 T>C), RS1001480146 (13:21160403 T>C)

Disease associations

OMIM: gene MIM:619247 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	4
Cadmium Chloride	decreases expression, increases abundance	3
Acetaminophen	decreases expression, increases expression	2
Benzo(a)pyrene	increases expression, increases methylation	2
Methotrexate	affects cotreatment, decreases expression	2
Valproic Acid	decreases expression	2
Aflatoxin B1	increases expression, increases methylation	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
FR900359	affects phosphorylation	1
bisphenol A	decreases expression	1
perfluorooctanoic acid	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
manganese chloride	increases abundance, increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	increases expression, affects cotreatment	1
phenethyl isothiocyanate	decreases expression	1
chromium hexavalent ion	decreases expression, increases abundance	1
2-palmitoylglycerol	increases expression	1
ICG 001	increases expression	1
jinfukang	increases expression	1
incobotulinumtoxinA	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Dasatinib	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ethanol	affects cotreatment, decreases expression, increases abundance	1
Atrazine	decreases expression	1
Cadmium	decreases expression, increases abundance	1
Caffeine	increases phosphorylation	1

Clinical trials (associated diseases)

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