KIAA1143

Summary

KIAA1143 (HGNC:29198) is a protein-coding gene on chromosome 3p21.31, encoding Uncharacterized protein KIAA1143 (Q96AT1). It is a selective cancer dependency (DepMap: 19.1% of cell lines).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 33 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 19.1% of screened cell lines
• MANE Select transcript: NM_020696

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29198
Approved symbol	KIAA1143
Name	KIAA1143
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000163807
Ensembl biotype	protein_coding
Entrez	57456

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000296121, ENST00000484437, ENST00000917638, ENST00000917639, ENST00000917640, ENST00000917641, ENST00000917642

RefSeq mRNA: 2 — MANE Select: NM_020696 NM_001320334, NM_020696

CCDS: CCDS2721

Canonical transcript exons

ENST00000296121 — 3 exons

Exon	Start	End
ENSE00001179350	44761495	44761619
ENSE00001339653	44748744	44753552
ENSE00003604612	44754224	44754368

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 97.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 62.2100 / max 1390.2749, expressed in 1820 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41863	56.8978	1820
41864	5.3123	1591

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.18	gold quality
adrenal tissue	UBERON:0018303	90.23	gold quality
corpus callosum	UBERON:0002336	89.51	gold quality
endometrium	UBERON:0001295	88.46	gold quality
skeletal muscle tissue	UBERON:0001134	87.99	gold quality
islet of Langerhans	UBERON:0000006	87.97	gold quality
ventricular zone	UBERON:0003053	87.92	gold quality
embryo	UBERON:0000922	87.76	gold quality
ganglionic eminence	UBERON:0004023	87.76	gold quality
smooth muscle tissue	UBERON:0001135	87.65	gold quality
skeletal muscle organ	UBERON:0014892	87.55	gold quality
muscle of leg	UBERON:0001383	87.54	gold quality
muscle tissue	UBERON:0002385	87.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	87.20	gold quality
gastrocnemius	UBERON:0001388	87.14	gold quality
cortical plate	UBERON:0005343	86.77	gold quality
colonic epithelium	UBERON:0000397	86.75	gold quality
left testis	UBERON:0004533	86.71	gold quality
placenta	UBERON:0001987	86.67	gold quality
leukocyte	CL:0000738	86.61	gold quality
monocyte	CL:0000576	86.50	gold quality
right testis	UBERON:0004534	86.39	gold quality
testis	UBERON:0000473	86.16	gold quality
bone element	UBERON:0001474	85.54	gold quality
bone marrow	UBERON:0002371	85.54	gold quality
vermiform appendix	UBERON:0001154	85.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.12	gold quality
prefrontal cortex	UBERON:0000451	84.97	gold quality
lymph node	UBERON:0000029	84.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

131 targeting KIAA1143, 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-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 19.1% of screened cell lines.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:77056	ENSDARG00000029615
mus_musculus	1110059G10Rik	ENSMUSG00000032551
rattus_norvegicus	RGD1311745	ENSRNOG00000004135
drosophila_melanogaster	CG42245	FBGN0250911
caenorhabditis_elegans	T25G3.1	WBGENE00012029

Protein

Protein identifiers

Uncharacterized protein KIAA1143 — Q96AT1 (reviewed: Q96AT1)

All UniProt accessions (1): Q96AT1

RefSeq proteins (2): NP_001307263, NP_065747* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027911	DUF4604	Domain
IPR040219	KIAA1143-like	Family

Pfam: PF15377

UniProt features (8 total): modified residue 3, region of interest 2, chain 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96AT1-F1	72.44	0.17

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 (3): 50, 108, 146

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 114 (showing top): YY1_Q6, E2F_Q3, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, YY1_02, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, BENPORATH_NOS_TARGETS, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, E2F1_Q3, SENESE_HDAC3_TARGETS_DN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, GCCATNTTG_YY1_Q6, BENPORATH_OCT4_TARGETS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, MARSON_BOUND_BY_E2F4_UNSTIMULATED, GOCC_INTERCELLULAR_BRIDGE

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

260 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA1143	TMEM204	Q9BSN7	721
KIAA1143	KLF12	Q9Y4X4	617
KIAA1143	SAMSN1	Q9NSI8	606
KIAA1143	CRTAM	O95727	570
KIAA1143	NRN1L	Q496H8	540
KIAA1143	ZNF790	Q6PG37	507
KIAA1143	CXCR3	P49682	481
KIAA1143	OR13C8	Q8NGS7	480
KIAA1143	TSTD1	Q8NFU3	461
KIAA1143	FCRL3	Q96P31	431
KIAA1143	SLC25A2	Q9BXI2	374
KIAA1143	JAKMIP2	Q96AA8	374
KIAA1143	ZC3H3	Q8IXZ2	369
KIAA1143	SHROOM4	Q9ULL8	352
KIAA1143	STYX	Q8WUJ0	348

IntAct

26 interactions, top by confidence:

A	B	Type	Score
CEP76	KIAA1143	psi-mi:“MI:0915”(physical association)	0.780
KIAA1143	CEP76	psi-mi:“MI:0915”(physical association)	0.780
KIAA1143	SNRNP200	psi-mi:“MI:0914”(association)	0.640
KIAA1143	AQR	psi-mi:“MI:0914”(association)	0.530
C1orf162	KIAA1143	psi-mi:“MI:0914”(association)	0.530
	KIAA1143	psi-mi:“MI:0407”(direct interaction)	0.440
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
NS	KIAA1143	psi-mi:“MI:0915”(physical association)	0.370
Crnkl1	PLRG1	psi-mi:“MI:0914”(association)	0.350
TBP	DYRK1A	psi-mi:“MI:0914”(association)	0.350
KIF15	DMD	psi-mi:“MI:0914”(association)	0.350
Junb	RGPD3	psi-mi:“MI:0914”(association)	0.350
MMGT1	DERL1	psi-mi:“MI:0914”(association)	0.350
SGTB	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
MAPT	MEX3A	psi-mi:“MI:0914”(association)	0.350
FGB	NME2	psi-mi:“MI:0914”(association)	0.350
C1orf162	CORO1A	psi-mi:“MI:0914”(association)	0.350
LMNA	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
KIAA1143	CEP76	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (91): CEP76 (Two-hybrid), KIAA1143 (Co-fractionation), KIAA1143 (Co-fractionation), KIAA1143 (Proximity Label-MS), CEP76 (Two-hybrid), KIAA1143 (Affinity Capture-MS), KIAA1143 (Affinity Capture-MS), KIAA1143 (Affinity Capture-MS), KIAA1143 (Affinity Capture-MS), KIAA1143 (Affinity Capture-MS), KIAA1143 (Affinity Capture-MS), AQR (Affinity Capture-MS), CRNKL1 (Affinity Capture-MS), XAB2 (Affinity Capture-MS), KIAA1143 (Affinity Capture-MS)

ESM2 similar proteins: A2AQ19, B5G1C4, B5XE27, O43290, O43395, O43768, P04975, P56211, P56212, P60840, P60841, P68210, P68211, Q02614, Q13435, Q1L8X2, Q28055, Q28GU6, Q2KIA6, Q2KIT1, Q3MHJ0, Q3U155, Q3UJB0, Q5PQS7, Q5R5J3, Q5RAD5, Q5XIW8, Q5ZIF8, Q5ZIH9, Q5ZJ85, Q5ZJ97, Q5ZLY8, Q6DEB4, Q6GQG3, Q6NVR1, Q6PII3, Q712U5, Q712U6, Q7ZXH9, Q8NDD1

Diamond homologs: Q3MHJ0, Q5RKH3, Q5XHI2, Q5ZJ97, Q8K039, Q96AT1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	26
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
442400	GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)	Pathogenic

SpliceAI

527 predictions. Top by Δscore:

Variant	Effect	Δscore
3:44753343:A:AC	donor_gain	1.0000
3:44753343:ACT:A	donor_gain	1.0000
3:44753344:C:CC	donor_gain	1.0000
3:44753344:CT:C	donor_gain	1.0000
3:44753344:CTC:C	donor_gain	1.0000
3:44754222:A:AC	donor_gain	1.0000
3:44754222:ACCTG:A	donor_gain	1.0000
3:44754223:C:CT	donor_gain	1.0000
3:44754223:CCTG:C	donor_gain	1.0000
3:44754223:CCTGC:C	donor_gain	1.0000
3:44754364:ATTCT:A	acceptor_gain	1.0000
3:44754365:TTCT:T	acceptor_gain	1.0000
3:44754365:TTCTC:T	acceptor_gain	1.0000
3:44754366:TCTCT:T	acceptor_gain	1.0000
3:44754367:CT:C	acceptor_gain	1.0000
3:44754367:CTCTA:C	acceptor_gain	1.0000
3:44754368:TC:T	acceptor_loss	1.0000
3:44754369:C:CC	acceptor_gain	1.0000
3:44754369:C:CG	acceptor_loss	1.0000
3:44761489:GCTCA:G	donor_loss	1.0000
3:44761490:CTCA:C	donor_loss	1.0000
3:44761491:TCA:T	donor_loss	1.0000
3:44761492:CAC:C	donor_loss	1.0000
3:44761882:AAA:A	donor_gain	1.0000
3:44761882:AAAGT:A	donor_loss	1.0000
3:44761883:AA:A	donor_gain	1.0000
3:44761883:AAG:A	donor_loss	1.0000
3:44761885:G:C	donor_loss	1.0000
3:44761885:G:GG	donor_gain	1.0000
3:44753344:CTCA:C	donor_gain	0.9900

AlphaMissense

1011 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:44761537:C:A	K22N	0.990
3:44761537:C:G	K22N	0.990
3:44761552:A:C	F17L	0.988
3:44761552:A:T	F17L	0.988
3:44761554:A:G	F17L	0.988
3:44753365:A:C	F147L	0.980
3:44753365:A:T	F147L	0.980
3:44753367:A:G	F147L	0.980
3:44761541:A:G	F21S	0.980
3:44761550:A:T	L18Q	0.967
3:44761553:A:G	F17S	0.965
3:44761495:C:A	K36N	0.960
3:44761495:C:G	K36N	0.960
3:44761553:A:C	F17C	0.958
3:44754301:A:T	V59E	0.952
3:44754277:A:G	L67P	0.948
3:44754298:A:T	V60E	0.948
3:44761559:G:T	P15Q	0.942
3:44761583:A:T	V7E	0.936
3:44761550:A:G	L18P	0.934
3:44761560:G:A	P15S	0.932
3:44754307:G:T	P57H	0.931
3:44754308:G:A	P57S	0.928
3:44761538:T:G	K22T	0.928
3:44761578:A:C	Y9D	0.927
3:44753372:A:G	L145P	0.922
3:44753372:A:T	L145H	0.917
3:44753517:A:C	Y97D	0.914
3:44761538:T:A	K22M	0.913
3:44761529:A:T	V25D	0.912

dbSNP variants (sampled 300 via entrez): RS1000020192 (3:44758701 A>G), RS1000039206 (3:44759624 C>T), RS1000198333 (3:44759058 C>G,T), RS1000327665 (3:44751461 G>A), RS1000380300 (3:44751863 G>A), RS1001014935 (3:44756898 G>A), RS1001116114 (3:44751015 G>T), RS1001322944 (3:44758655 T>G), RS1002017319 (3:44755303 A>C,G), RS1002216942 (3:44755589 C>T), RS1003104480 (3:44760670 G>A), RS1003216679 (3:44748268 A>G), RS1003294850 (3:44760464 A>C), RS1003295155 (3:44749531 A>C), RS1003607679 (3:44757321 T>C)

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

1 associations (top):

Study	Trait	p-value
GCST008103_52	Bipolar disorder	3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	increases expression, decreases expression	1
triphenyl phosphate	affects expression	1
uranyl acetate	increases expression	1
bisphenol A	decreases methylation	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
K 7174	increases expression	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, increases expression	1
MT19c compound	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Caffeine	increases phosphorylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Tretinoin	decreases expression	1
Uranium	increases expression	1
Valproic Acid	decreases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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