KTI12

Summary

KTI12 (KTI12 chromatin associated homolog, HGNC:25160) is a protein-coding gene on chromosome 1p32.3, encoding Protein KTI12 homolog (Q96EK9). It is a selective cancer dependency (DepMap: 88.6% of cell lines).

Predicted to enable ATP binding activity. Predicted to be involved in tRNA wobble uridine modification.

Source: NCBI Gene 112970 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 55 total
• Cancer dependency (DepMap): dependent in 88.6% of screened cell lines
• MANE Select transcript: NM_138417

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25160
Approved symbol	KTI12
Name	KTI12 chromatin associated homolog
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	TOT4, MGC20419, SBBI81
Ensembl gene	ENSG00000198841
Ensembl biotype	protein_coding
Entrez	112970

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000371614

RefSeq mRNA: 1 — MANE Select: NM_138417 NM_138417

CCDS: CCDS562

Canonical transcript exons

ENST00000371614 — 1 exons

Exon	Start	End
ENSE00001455669	52032103	52033810

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 89.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.5008 / max 98.8867, expressed in 1796 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12345	10.9965	1796
12344	0.5043	214

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.06	gold quality
granulocyte	CL:0000094	81.73	gold quality
stromal cell of endometrium	CL:0002255	81.27	gold quality
leukocyte	CL:0000738	80.90	gold quality
monocyte	CL:0000576	80.80	gold quality
left adrenal gland	UBERON:0001234	80.48	gold quality
right adrenal gland	UBERON:0001233	80.42	gold quality
right adrenal gland cortex	UBERON:0035827	80.27	gold quality
left adrenal gland cortex	UBERON:0035825	79.97	gold quality
mucosa of transverse colon	UBERON:0004991	79.54	gold quality
islet of Langerhans	UBERON:0000006	78.88	gold quality
adrenal gland	UBERON:0002369	78.23	gold quality
left uterine tube	UBERON:0001303	78.17	gold quality
adrenal cortex	UBERON:0001235	77.98	gold quality
descending thoracic aorta	UBERON:0002345	77.48	gold quality
right ovary	UBERON:0002118	76.83	gold quality
vermiform appendix	UBERON:0001154	76.51	gold quality
body of stomach	UBERON:0001161	76.38	gold quality
left ovary	UBERON:0002119	76.36	gold quality
thoracic aorta	UBERON:0001515	76.32	gold quality
lower esophagus muscularis layer	UBERON:0035833	76.27	gold quality
lower esophagus	UBERON:0013473	76.24	gold quality
left coronary artery	UBERON:0001626	76.17	gold quality
spleen	UBERON:0002106	76.05	gold quality
ascending aorta	UBERON:0001496	76.04	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.01	gold quality
transverse colon	UBERON:0001157	75.84	gold quality
aorta	UBERON:0000947	75.66	gold quality
popliteal artery	UBERON:0002250	75.49	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting KTI12, 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-548P	99.98	72.25	3784
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-325	99.58	66.55	358
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-217-5P	99.49	69.93	1419
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-4796-3P	99.08	68.38	1681
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-4704-3P	98.28	69.33	1300
HSA-MIR-3909	97.55	66.78	887
HSA-MIR-4661-3P	96.81	66.02	342
HSA-MIR-4683	95.29	65.98	631
HSA-MIR-877-5P	94.62	66.30	710
HSA-MIR-4746-5P	94.32	69.49	70
HSA-MIR-12115	94.19	66.37	738

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 88.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• Same but different - Molecular comparison of human KTI12 and PSTK. (PMID:33417976)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	kti12	ENSDARG00000054301
mus_musculus	Kti12	ENSMUSG00000073775
rattus_norvegicus	Kti12	ENSRNOG00000070073
drosophila_melanogaster	CG3587	FBGN0023521
caenorhabditis_elegans		WBGENE00013332

Protein

Protein identifiers

Protein KTI12 homolog — Q96EK9 (reviewed: Q96EK9)

All UniProt accessions (1): Q96EK9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the KTI12 family.

RefSeq proteins (1): NP_612426* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013641	KTI12/PSTK	Family
IPR027417	P-loop_NTPase	Homologous_superfamily

Pfam: PF08433

UniProt features (8 total): region of interest 2, modified residue 2, chain 1, compositionally biased region 1, binding site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96EK9-F1	75.18	0.45

Functional residue map

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

Ligand- & substrate-binding residues (1): 8–15

Post-translational modifications (2): 184, 200

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GOBP_TRNA_METABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_RNA_MODIFICATION, NRF2_01, GOBP_TRNA_PROCESSING, GOBP_TRNA_MODIFICATION, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, SCGGAAGY_ELK1_02, GOMF_ADENYL_NUCLEOTIDE_BINDING, GOBP_TRNA_WOBBLE_BASE_MODIFICATION, LEE_BMP2_TARGETS_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, ESC_J1_UP_EARLY.V1_DN

GO Biological Process (1): tRNA wobble uridine modification (GO:0002098)

GO Molecular Function (3): ATP binding (GO:0005524), nucleotide binding (GO:0000166), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tRNA wobble base modification	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1

Protein interactions and networks

STRING

848 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KTI12	ELP1	O95163	833
KTI12	ELP3	Q9H9T3	805
KTI12	ELP4	Q96EB1	800
KTI12	DPH3	Q96FX2	798
KTI12	MOCS3	O95396	717
KTI12	PSTK	Q8IV42	687
KTI12	CTU1	Q7Z7A3	682
KTI12	URM1	Q9BTM9	681
KTI12	PPP6R1	Q9UPN7	637
KTI12	PPP6R2	O75170	632
KTI12	PPP6R3	Q5H9R7	613
KTI12	ELP5	Q8TE02	564
KTI12	MCM5	P33992	561
KTI12	LZIC	Q8WZA0	540
KTI12	TMEM144	Q7Z5S9	538

IntAct

8 interactions, top by confidence:

A	B	Type	Score
FHL3	KTI12	psi-mi:“MI:0915”(physical association)	0.560
KTI12	FHL3	psi-mi:“MI:0915”(physical association)	0.560
GPR35	ATP5F1B	psi-mi:“MI:0914”(association)	0.530
GPR35	LGALS3	psi-mi:“MI:0914”(association)	0.530
ELP3	ACACB	psi-mi:“MI:0914”(association)	0.350
SNW1		psi-mi:“MI:0914”(association)	0.350

BioGRID (46): KTI12 (Two-hybrid), KTI12 (Affinity Capture-MS), KTI12 (Co-fractionation), KTI12 (Affinity Capture-MS), KTI12 (Affinity Capture-MS), KTI12 (Affinity Capture-MS), KTI12 (Affinity Capture-MS), KTI12 (Affinity Capture-MS), KTI12 (Affinity Capture-MS), KTI12 (Negative Genetic), KTI12 (Negative Genetic), KTI12 (Negative Genetic), MAGED2 (Co-fractionation), KTI12 (Affinity Capture-MS), IKBKAP (Affinity Capture-Western)

ESM2 similar proteins: A5WVX1, A6H784, A8MPP1, D3ZU57, O08600, O08644, O09127, O15197, O19179, O55171, O88941, P08466, P0C0K6, P28339, P29322, P38447, P51840, P51976, P52785, P54760, P54761, P55203, P81203, P81204, Q00653, Q02846, Q08DH8, Q0IH72, Q10480, Q10RZ1, Q14249, Q1HG60, Q2KIF8, Q2TBI4, Q3U6U5, Q502K1, Q80SX8, Q80UM7, Q8BYM8, Q8C163

Diamond homologs: B8BK80, B9GAG9, P34253, Q0P457, Q148I5, Q4KLF3, Q5I0L7, Q96EK9, Q9D1R2, Q9LMH0, Q9P7V4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

72 predictions. Top by Δscore:

Variant	Effect	Δscore
1:52033740:C:CT	acceptor_gain	0.9100
1:52033740:C:T	acceptor_gain	0.8300
1:52032689:T:TA	donor_gain	0.7800
1:52032720:A:AC	donor_gain	0.7100
1:52032721:C:CC	donor_gain	0.7100
1:52032850:TGTGG:T	donor_gain	0.6000
1:52032682:C:A	donor_gain	0.5200
1:52032684:C:T	donor_gain	0.4900
1:52032685:T:TT	donor_gain	0.4700
1:52032931:G:GT	donor_gain	0.4100
1:52032902:T:TA	donor_gain	0.4000
1:52032928:CGTG:C	donor_gain	0.3900
1:52032443:TGTC:T	donor_gain	0.3800
1:52032446:C:CT	donor_gain	0.3400
1:52032679:C:A	donor_gain	0.3400
1:52032923:TG:T	donor_gain	0.3400
1:52032930:TG:T	donor_gain	0.3400
1:52032920:A:AC	donor_gain	0.3300
1:52032921:C:CC	donor_gain	0.3300
1:52032690:C:G	donor_gain	0.3200
1:52032903:C:A	donor_gain	0.3200
1:52032929:G:GC	donor_gain	0.3200
1:52032689:TCCTC:T	donor_gain	0.3100
1:52032926:CTCG:C	donor_gain	0.3100
1:52032927:TCGT:T	donor_gain	0.3100
1:52033127:AGGG:A	donor_gain	0.3100
1:52032678:TCCC:T	donor_gain	0.3000
1:52032679:CCCC:C	donor_gain	0.3000
1:52032680:CCCC:C	donor_gain	0.3000
1:52032681:CCCC:C	donor_gain	0.3000

AlphaMissense

2260 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:52033087:C:A	W225C	0.998
1:52033087:C:G	W225C	0.998
1:52033089:A:G	W225R	0.998
1:52033089:A:T	W225R	0.998
1:52032787:A:C	F325L	0.997
1:52032787:A:T	F325L	0.997
1:52032788:A:G	F325S	0.997
1:52032789:A:G	F325L	0.997
1:52032728:A:G	F345S	0.995
1:52033508:T:A	K85I	0.995
1:52033516:G:C	N82K	0.994
1:52033516:G:T	N82K	0.994
1:52032727:A:C	F345L	0.993
1:52032727:A:T	F345L	0.993
1:52032729:A:G	F345L	0.993
1:52032929:G:T	T278K	0.992
1:52033086:C:G	D226H	0.992
1:52032809:A:G	L318P	0.991
1:52033085:T:A	D226V	0.991
1:52033507:T:A	K85N	0.991
1:52033507:T:G	K85N	0.991
1:52032794:C:G	R323P	0.990
1:52032797:C:G	R322P	0.990
1:52032798:G:T	R322S	0.990
1:52033497:A:G	Y89H	0.990
1:52033500:G:T	R88S	0.990
1:52033506:C:G	G86R	0.990
1:52033085:T:G	D226A	0.989
1:52033106:G:T	P219H	0.989
1:52033501:G:C	F87L	0.989

dbSNP variants (sampled 300 via entrez): RS1000969069 (1:52033560 G>A), RS1001617907 (1:52034269 A>C), RS1001940561 (1:52032566 G>A,C), RS1001973064 (1:52032300 G>C,T), RS1003474049 (1:52034995 C>T), RS1003540551 (1:52035753 C>T), RS1003548355 (1:52033612 G>A), RS1003746159 (1:52034775 A>T), RS1004911567 (1:52035048 G>A), RS1005574366 (1:52032225 T>C), RS1005606985 (1:52031852 G>A), RS1006538577 (1:52034654 G>A,C), RS1009554453 (1:52035574 G>A,C,T), RS1010815962 (1:52034722 G>A,T), RS1010845711 (1:52034235 G>A)

Disease associations

OMIM: gene `` | 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

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression	2
di-n-butylphosphoric acid	affects expression	1
2,6-dichloro-(1,4)benzoquinone	increases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Formaldehyde	decreases expression	1
Quercetin	decreases expression	1
Rotenone	increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression, increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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