KIAA2013

Summary

KIAA2013 (HGNC:28513) is a protein-coding gene on chromosome 1p36.22, encoding Uncharacterized protein KIAA2013 (Q8IYS2). It is a selective cancer dependency (DepMap: 12.5% of cell lines).

Located in membrane.

Source: NCBI Gene 90231 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 104 total
• Cancer dependency (DepMap): dependent in 12.5% of screened cell lines
• MANE Select transcript: NM_138346

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28513
Approved symbol	KIAA2013
Name	KIAA2013
Location	1p36.22
Locus type	gene with protein product
Status	Approved
Aliases	MGC33867, RP5-1077B9.1
Ensembl gene	ENSG00000116685
Ensembl biotype	protein_coding
Entrez	90231

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000376572, ENST00000376576, ENST00000923856, ENST00000966533

RefSeq mRNA: 1 — MANE Select: NM_138346 NM_138346

CCDS: CCDS141

Canonical transcript exons

ENST00000376572 — 3 exons

Exon	Start	End
ENSE00001323263	11922636	11923489
ENSE00001470961	11919591	11920332
ENSE00001470962	11925205	11926427

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 97.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.9469 / max 178.4977, expressed in 1805 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
10348	17.9469	1805

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	97.67	gold quality
kidney epithelium	UBERON:0004819	96.72	gold quality
oviduct epithelium	UBERON:0004804	95.75	gold quality
left ventricle myocardium	UBERON:0006566	95.35	silver quality
mucosa of transverse colon	UBERON:0004991	94.92	gold quality
upper arm skin	UBERON:0004263	94.45	gold quality
cardiac muscle of right atrium	UBERON:0003379	94.31	silver quality
tibialis anterior	UBERON:0001385	93.72	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.07	gold quality
duodenum	UBERON:0002114	93.05	gold quality
small intestine Peyer’s patch	UBERON:0003454	92.91	gold quality
descending thoracic aorta	UBERON:0002345	92.74	gold quality
blood	UBERON:0000178	92.65	gold quality
medial globus pallidus	UBERON:0002477	92.64	gold quality
granulocyte	CL:0000094	92.61	gold quality
apex of heart	UBERON:0002098	92.61	gold quality
epithelial cell of pancreas	CL:0000083	92.51	gold quality
stromal cell of endometrium	CL:0002255	92.50	gold quality
transverse colon	UBERON:0001157	92.50	gold quality
small intestine	UBERON:0002108	92.50	gold quality
nasal cavity epithelium	UBERON:0005384	92.50	gold quality
tendon of biceps brachii	UBERON:0008188	92.38	gold quality
secondary oocyte	CL:0000655	92.22	gold quality
right lobe of liver	UBERON:0001114	92.16	gold quality
gastrocnemius	UBERON:0001388	92.16	gold quality
thoracic aorta	UBERON:0001515	92.15	gold quality
ascending aorta	UBERON:0001496	92.06	gold quality
right coronary artery	UBERON:0001625	91.96	gold quality
aorta	UBERON:0000947	91.94	gold quality
quadriceps femoris	UBERON:0001377	91.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	39.77
E-ANND-3	yes	5.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

70 targeting KIAA2013, 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-9-5P	100.00	72.28	2361
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-609	99.82	64.26	505
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-6794-5P	99.76	66.38	1048

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.5% of screened cell lines.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkeyp-104h9.5	ENSDARG00000073801
mus_musculus	2510039O18Rik	ENSMUSG00000044496
rattus_norvegicus	2510039O18Rikl	ENSRNOG00000007968
drosophila_melanogaster	CG7289	FBGN0031379
caenorhabditis_elegans		WBGENE00015928

Protein

Protein identifiers

Uncharacterized protein KIAA2013 — Q8IYS2 (reviewed: Q8IYS2)

All UniProt accessions (1): Q8IYS2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IYS2-1	1	yes
Q8IYS2-2	2

RefSeq proteins (1): NP_612355* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018795	K2013-like	Family

Pfam: PF10222

UniProt features (7 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, glycosylation site 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYS2-F1	85.77	0.61

Functional residue map

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

Glycosylation sites (1): 363

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): WANG_CLIM2_TARGETS_UP, MODULE_255, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MENSE_HYPOXIA_UP, MODULE_317, GTGCCTT_MIR506, WANG_LMO4_TARGETS_DN, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GCM_NF2, LEE_CALORIE_RESTRICTION_NEOCORTEX_UP, ETF_Q6, MODULE_69, NUYTTEN_NIPP1_TARGETS_DN, chr1p36

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

924 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA2013	MBLAC2	Q68D91	591
KIAA2013	HECTD3	Q5T447	552
KIAA2013	MYO1D	O94832	535
KIAA2013	GET3	O43681	526
KIAA2013	PLOD1	Q02809	514
KIAA2013	PDXDC1	Q6P996	505
KIAA2013	MIIP	Q5JXC2	488
KIAA2013	ESYT2	A0FGR8	479
KIAA2013	ATP5MJ	P56378	476
KIAA2013	ASRGL1	Q7L266	475
KIAA2013	VPS13D	Q5THJ4	474
KIAA2013	OTUD4	Q01804	458
KIAA2013	RCC2	Q9P258	455
KIAA2013	ATP5MC1	P05496	447
KIAA2013	FBXO2	Q9UK22	443

IntAct

165 interactions, top by confidence:

A	B	Type	Score
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
B3GAT3	GOLIM4	psi-mi:“MI:0914”(association)	0.640
TCIRG1	ATP6AP2	psi-mi:“MI:0914”(association)	0.640
TRDN	TMEM223	psi-mi:“MI:0914”(association)	0.640
IGFBP5	KIAA2013	psi-mi:“MI:0915”(physical association)	0.560
KIAA2013	TMEM60	psi-mi:“MI:0915”(physical association)	0.560
PICK1	ILVBL	psi-mi:“MI:0914”(association)	0.530
CSGALNACT2	GOLIM4	psi-mi:“MI:0914”(association)	0.530
ATP6V0A2	B4GALT3	psi-mi:“MI:0914”(association)	0.530
CHRND	TPST2	psi-mi:“MI:0914”(association)	0.530
ATP6V0A1	ATP6AP2	psi-mi:“MI:0914”(association)	0.530
KIAA2013	TMBIM6	psi-mi:“MI:0914”(association)	0.530
CCR6	PODXL	psi-mi:“MI:0914”(association)	0.530
TMEM63A	AP3D1	psi-mi:“MI:0914”(association)	0.530
KIAA2013	ATP6AP2	psi-mi:“MI:0914”(association)	0.530
ATP6V0A4	ATP6AP2	psi-mi:“MI:0914”(association)	0.530
CHRNA4	FZD6	psi-mi:“MI:0914”(association)	0.530
CSGALNACT2	TPST1	psi-mi:“MI:0914”(association)	0.530
GPRC5B	STXBP3	psi-mi:“MI:0914”(association)	0.530
SLC7A1	STXBP3	psi-mi:“MI:0914”(association)	0.530
TMEM106A	B4GALT3	psi-mi:“MI:0914”(association)	0.530
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
KIAA2013	HNRNPAB	psi-mi:“MI:0915”(physical association)	0.400
KIAA2013	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
KIAA2013	ADRA1A	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (191): KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS), KIAA2013 (Affinity Capture-MS)

ESM2 similar proteins: A6NE02, A8MY62, C9JR72, D3Z7H8, D3ZU57, O09017, O15197, O19179, O95382, P0C0K6, P10588, P43136, P55203, Q02846, Q08DG4, Q15628, Q2KHV9, Q3U0S6, Q3UH93, Q5BK61, Q5U651, Q5W7P8, Q5ZMM1, Q6ZNJ1, Q6ZQA0, Q6ZVZ8, Q80ZD5, Q86WK7, Q8BH02, Q8BH83, Q8C828, Q8CIG9, Q8IUL8, Q8IYS2, Q8JGM4, Q8K2J9, Q8N239, Q8VHA6, Q91X21, Q96CD0

Diamond homologs: A4IH88, Q2KHV9, Q6DDG2, Q8IYS2, Q91X21

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 222 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
Lysosphingolipid and LPA receptors	5	27.2×	3e-04
Insulin receptor recycling	5	13.6×	4e-03
Transferrin endocytosis and recycling	5	13.2×	4e-03
ROS and RNS production in phagocytes	5	12.0×	6e-03
Class A/1 (Rhodopsin-like receptors)	15	8.0×	4e-07
GPCR ligand binding	12	5.5×	4e-04
SLC-mediated transmembrane transport	10	4.2×	9e-03
Signaling by GPCR	14	4.0×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
vacuolar acidification	5	19.9×	1e-03
positive regulation of cytosolic calcium ion concentration	15	9.5×	7e-08
adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	8	9.5×	7e-04
phospholipase C-activating G protein-coupled receptor signaling pathway	13	9.3×	1e-06
transmembrane transport	8	7.3×	3e-03
cell chemotaxis	7	7.0×	8e-03
carbohydrate metabolic process	9	6.7×	2e-03
chemotaxis	8	5.9×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	98
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

473 predictions. Top by Δscore:

Variant	Effect	Δscore
1:11923487:CTC:C	acceptor_gain	1.0000
1:11923488:TCCTG:T	acceptor_loss	1.0000
1:11923490:C:CC	acceptor_gain	1.0000
1:11923491:T:C	acceptor_loss	1.0000
1:11925200:CTCA:C	donor_loss	1.0000
1:11925201:TCA:T	donor_loss	1.0000
1:11925202:CAC:C	donor_loss	1.0000
1:11925204:C:CT	donor_loss	1.0000
1:11923485:CACTC:C	acceptor_gain	0.9900
1:11923486:ACTC:A	acceptor_gain	0.9900
1:11923487:CTCC:C	acceptor_gain	0.9900
1:11923488:TC:T	acceptor_gain	0.9900
1:11923488:TCCT:T	acceptor_gain	0.9900
1:11923489:CC:C	acceptor_gain	0.9900
1:11923496:CACCA:C	acceptor_gain	0.9900
1:11923499:C:CT	acceptor_gain	0.9900
1:11925203:A:AC	donor_gain	0.9900
1:11925204:C:CC	donor_gain	0.9900
1:11923499:C:T	acceptor_gain	0.9800
1:11925203:AC:A	donor_gain	0.9800
1:11925204:CC:C	donor_gain	0.9800
1:11925204:CCT:C	donor_gain	0.9700
1:11925204:CCTGG:C	donor_gain	0.9700
1:11923498:CCA:C	acceptor_gain	0.9600
1:11923500:A:C	acceptor_gain	0.9500
1:11925204:CCTG:C	donor_gain	0.9500
1:11922639:ACT:A	donor_gain	0.9400
1:11922640:CTC:C	donor_gain	0.9400
1:11923493:C:CT	acceptor_gain	0.9400
1:11923500:A:T	acceptor_gain	0.9400

AlphaMissense

4045 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:11922707:G:C	H606D	0.999
1:11922732:G:C	S597R	0.999
1:11922732:G:T	S597R	0.999
1:11922734:T:G	S597R	0.999
1:11923235:A:G	W430R	0.999
1:11923235:A:T	W430R	0.999
1:11922688:A:G	L612P	0.998
1:11922706:T:C	H606R	0.998
1:11922708:G:C	F605L	0.998
1:11922708:G:T	F605L	0.998
1:11922710:A:G	F605L	0.998
1:11923152:G:C	S457R	0.998
1:11923152:G:T	S457R	0.998
1:11923154:T:G	S457R	0.998
1:11923222:A:G	L434P	0.998
1:11923284:C:A	W413C	0.998
1:11923284:C:G	W413C	0.998
1:11923286:A:G	W413R	0.998
1:11923286:A:T	W413R	0.998
1:11923320:G:C	F401L	0.998
1:11923320:G:T	F401L	0.998
1:11923322:A:G	F401L	0.998
1:11925608:G:C	N210K	0.998
1:11925608:G:T	N210K	0.998
1:11922697:A:T	L609H	0.997
1:11922703:A:G	L607P	0.997
1:11922727:G:T	A599D	0.997
1:11922740:A:G	W595R	0.997
1:11922740:A:T	W595R	0.997
1:11922851:A:G	S558P	0.997

dbSNP variants (sampled 300 via entrez): RS1000323305 (1:11925444 GCCA>G), RS1000569031 (1:11924994 T>C), RS1000829410 (1:11919740 C>T), RS1001064270 (1:11923766 C>A), RS1001499995 (1:11924906 T>A), RS1001741421 (1:11924549 T>C), RS1002213736 (1:11926824 G>A), RS1002265947 (1:11926606 C>T), RS1003002266 (1:11923207 C>T), RS1003493201 (1:11922313 C>T), RS1003535487 (1:11927446 C>T), RS1003746327 (1:11921916 C>A), RS1004565543 (1:11924521 C>G,T), RS1004601254 (1:11927799 A>G), RS1004951155 (1:11928149 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): Charcot-Marie-Tooth disease type 2 (MONDO:0018993)

Orphanet (1): Autosomal dominant Charcot-Marie-Tooth disease type 2 (Orphanet:64746)

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST004923_1	Tuberculosis	1.000000e-11
GCST006137_4	Serum folate levels	2.000000e-07
GCST006166_98	Diastolic blood pressure x alcohol consumption interaction (2df test)	6.000000e-15
GCST006167_32	Mean arterial pressure x alcohol consumption interaction (2df test)	1.000000e-09
GCST006169_6	Diastolic blood pressure x alcohol consumption (light vs heavy) interaction (2df test)	3.000000e-09
GCST006434_102	Systolic blood pressure x alcohol consumption interaction (2df test)	1.000000e-15
GCST006434_74	Systolic blood pressure x alcohol consumption interaction (2df test)	6.000000e-21
GCST006585_101	Blood protein levels	2.000000e-12
GCST007580_2	Red blood cell folate levels	5.000000e-08
GCST008155_56	Waist-hip ratio	5.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004329	alcohol drinking
EFO:0006336	diastolic blood pressure
EFO:0006340	mean arterial pressure
EFO:0006335	systolic blood pressure
EFO:0004343	waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
perfluorooctanoic acid	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
abrine	decreases expression	1
Temozolomide	increases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Cadmium	increases abundance, increases palmitoylation, decreases reaction	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Asbestos, Crocidolite	increases expression	1
Cadmium Chloride	increases palmitoylation, decreases reaction, increases abundance	1
Palmitic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05902351	Not specified	RECRUITING	Natural History Study for Charcot Marie Tooth Disease