KIAA0040

Summary

KIAA0040 (HGNC:28950) is a protein-coding gene on chromosome 1q25.1, encoding Uncharacterized protein KIAA0040 (Q15053).

Predicted to be located in membrane.

Source: NCBI Gene 9674 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 13 total
• MANE Select transcript: NM_014656

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28950
Approved symbol	KIAA0040
Name	KIAA0040
Location	1q25.1
Locus type	gene with protein product
Status	Approved
Aliases	IAMP
Ensembl gene	ENSG00000235750
Ensembl biotype	protein_coding
OMIM	616696
Entrez	9674

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000423313, ENST00000444639, ENST00000545251, ENST00000563563, ENST00000567124, ENST00000619513, ENST00000868056, ENST00000868057, ENST00000868058, ENST00000868059, ENST00000868060, ENST00000868061, ENST00000868062, ENST00000868063, ENST00000868064, ENST00000868065, ENST00000868066, ENST00000868067, ENST00000868068, ENST00000951829

RefSeq mRNA: 6 — MANE Select: NM_014656 NM_001162893, NM_001162894, NM_001162895, NM_001319230, NM_001319231, NM_014656

CCDS: CCDS86034

Canonical transcript exons

ENST00000423313 — 4 exons

Exon	Start	End
ENSE00001611129	175177611	175177684
ENSE00001633667	175166562	175166737
ENSE00001682888	175192640	175192776
ENSE00003842935	175156986	175161146

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 93.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.1889 / max 176.9023, expressed in 1065 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15989	5.6537	868
15990	0.6794	386
15991	0.6474	294
15992	0.6332	355
15993	0.4173	223
15987	0.1579	72

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lung	UBERON:0002167	93.42	gold quality
calcaneal tendon	UBERON:0003701	92.67	gold quality
blood	UBERON:0000178	92.44	gold quality
upper lobe of left lung	UBERON:0008952	92.05	gold quality
placenta	UBERON:0001987	91.86	gold quality
upper lobe of lung	UBERON:0008948	91.65	gold quality
granulocyte	CL:0000094	91.35	gold quality
mucosa of stomach	UBERON:0001199	91.31	gold quality
parotid gland	UBERON:0001831	91.10	gold quality
leukocyte	CL:0000738	90.29	gold quality
omental fat pad	UBERON:0010414	90.19	gold quality
peritoneum	UBERON:0002358	90.16	gold quality
monocyte	CL:0000576	90.01	gold quality
lower lobe of lung	UBERON:0008949	89.99	gold quality
mononuclear cell	CL:0000842	89.89	gold quality
adipose tissue of abdominal region	UBERON:0007808	89.88	gold quality
lymph node	UBERON:0000029	89.77	gold quality
gall bladder	UBERON:0002110	89.31	gold quality
decidua	UBERON:0002450	89.04	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.83	gold quality
vermiform appendix	UBERON:0001154	88.56	gold quality
adipose tissue	UBERON:0001013	88.50	gold quality
body of pancreas	UBERON:0001150	88.38	gold quality
lung	UBERON:0002048	88.27	gold quality
spleen	UBERON:0002106	87.90	gold quality
connective tissue	UBERON:0002384	87.90	gold quality
colonic epithelium	UBERON:0000397	87.84	gold quality
metanephros cortex	UBERON:0010533	87.76	gold quality
left uterine tube	UBERON:0001303	87.64	gold quality
pancreas	UBERON:0001264	87.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	26.86
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting KIAA0040, 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-6867-5P	100.00	82.21	3464
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782

Literature-anchored findings (GeneRIF, showing 3)

• Several flanking SNPs of the top hits in the meta-analysis demonstrated borderline associations with alcohol dependence in the family sample for KIAA0040, NRD1 and THSD7B, respectively. (PMID:21703634)
• conclude that KIAA0040 might harbor a causal variant for AD and thus might directly contribute to risk for this disorder. (PMID:21956439)
• KIAA0040 enhances glioma growth by controlling the JAK2/STAT3 signalling pathway. (PMID:38661644)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	4930523C07Rik	ENSMUSG00000090394
rattus_norvegicus	Kiaa0040	ENSRNOG00000049537

Protein

Protein identifiers

Uncharacterized protein KIAA0040 — Q15053 (reviewed: Q15053)

All UniProt accessions (2): Q15053, A0A384DVV8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (6): NP_001156365, NP_001156366, NP_001156367, NP_001306159, NP_001306160, NP_055471* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039964	KIAA0040-like	Family

UniProt features (5 total): chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15053-F1	69.05	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 196 (showing top): GGGACCA_MIR133A_MIR133B, ATACCTC_MIR202, CAIRO_HEPATOBLASTOMA_CLASSES_DN, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, MODULE_497, TGGNNNNNNKCCAR_UNKNOWN, RYTTCCTG_ETS2_B, LOPEZ_MESOTHELIOMA_SURVIVAL_UP, MODULE_112, ZHAN_MULTIPLE_MYELOMA_CD1_DN, MODULE_342, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, STEIN_ESRRA_TARGETS_UP, YOSHIMURA_MAPK8_TARGETS_DN

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

384 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA0040	TEX50	A0A1B0GTY4	585
KIAA0040	SERINC2	Q96SA4	581
KIAA0040	PKNOX2	Q96KN3	524
KIAA0040	ZBTB37	Q5TC79	491
KIAA0040	ANKRD45	Q5TZF3	476
KIAA0040	ZNF319	Q9P2F9	439
KIAA0040	THSD7B	Q9C0I4	419
KIAA0040	PHF3	Q92576	418
KIAA0040	C9orf152	Q5JTZ5	410
KIAA0040	ANKRD13C-DT	Q9XRX5	402
KIAA0040	SLC9C2	Q5TAH2	382
KIAA0040	TAS2R16	Q9NYV7	380
KIAA0040	ASTN1	O14525	370
KIAA0040	NPIPB15	A6NHN6	370
KIAA0040	C8orf58	Q8NAV2	369
KIAA0040	PRR15L	Q9BU68	369

IntAct

0 interactions, top by confidence:

BioGRID (9): KIAA0040 (Two-hybrid), KRTAP10-3 (Two-hybrid), KIAA0040 (Two-hybrid), KIAA0040 (Two-hybrid), KIAA0040 (Two-hybrid), KIAA0040 (Proximity Label-MS), KIAA0040 (Proximity Label-MS), KIAA0040 (Proximity Label-MS), KIAA0040 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GRQ0, A0A1B0GSZ0, A0A1B0GVT2, A0A590UK83, A0PK05, A2VDU1, A2VE22, A4QNL6, A5D7B5, A5D992, O43609, O75324, P0DKX4, P29414, P61807, P61808, Q0VFM5, Q15053, Q16655, Q17Q87, Q1L0X2, Q2KIK3, Q2TBG9, Q3MHM8, Q498C7, Q4V921, Q58CU5, Q5RBD8, Q5RF07, Q5RGQ8, Q64448, Q6UWT2, Q80ZU4, Q8BGN6, Q8BUM6, Q8C3K5, Q8C817, Q8K1D8, Q8N6S5, Q91VT8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

492 predictions. Top by Δscore:

Variant	Effect	Δscore
1:175192635:CTCA:C	donor_loss	1.0000
1:175192636:TCA:T	donor_loss	1.0000
1:175192637:CAC:C	donor_loss	1.0000
1:175192638:A:AC	donor_gain	1.0000
1:175192639:C:CC	donor_gain	1.0000
1:175192639:C:CG	donor_loss	1.0000
1:175177609:A:AC	donor_gain	0.9900
1:175177610:C:CC	donor_gain	0.9900
1:175192638:AC:A	donor_gain	0.9900
1:175192639:CC:C	donor_gain	0.9900
1:175192639:CCTTT:C	donor_gain	0.9900
1:175160704:T:TA	donor_gain	0.9800
1:175177610:CT:C	donor_gain	0.9800
1:175189054:T:C	donor_gain	0.9800
1:175192639:CCT:C	donor_gain	0.9800
1:175192639:CCTT:C	donor_gain	0.9800
1:175160713:A:C	donor_gain	0.9600
1:175177610:CTCA:C	donor_gain	0.9400
1:175192661:T:TA	donor_gain	0.9300
1:175177681:CAAT:C	acceptor_gain	0.9200
1:175160678:AGCC:A	donor_gain	0.9000
1:175160678:AGC:A	donor_gain	0.8900
1:175177613:A:AC	donor_gain	0.8900
1:175177610:CTCAG:C	donor_gain	0.8800
1:175160509:G:C	donor_gain	0.8700
1:175160787:T:TA	donor_gain	0.8700
1:175177614:G:C	donor_gain	0.8600
1:175166619:T:TA	donor_gain	0.8500
1:175189130:T:TA	donor_gain	0.8500
1:175160718:A:C	donor_gain	0.8400

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000334190 (1:175192502 C>A), RS1000405267 (1:175162123 C>T), RS1000490125 (1:175192971 C>T), RS1000549416 (1:175181532 T>C,G), RS1000551454 (1:175156793 C>T), RS1000682774 (1:175185478 G>A), RS1000686584 (1:175179582 G>C), RS1000690601 (1:175191850 A>G), RS1000754884 (1:175193145 C>G,T), RS1000930756 (1:175173392 T>A,G), RS1001056977 (1:175162685 C>T), RS1001087629 (1:175162449 C>T), RS1001091171 (1:175173023 A>G), RS1001137543 (1:175186525 T>C), RS1001230250 (1:175191408 T>C)

Disease associations

OMIM: gene MIM:616696 | 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
GCST001121_1	Alcohol dependence	2.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	3
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
ferrous chloride	decreases expression	1
Am 580	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Irinotecan	increases expression	1
Rosiglitazone	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Cisplatin	increases expression	1
Diethylhexyl Phthalate	increases expression	1
Doxorubicin	decreases expression	1
Fluorouracil	increases expression	1
Nickel	decreases expression	1
Selenium	increases expression	1
Silicon Dioxide	increases expression	1

Clinical trials (associated diseases)

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