NKIRAS1

Summary

NKIRAS1 (NFKB inhibitor interacting Ras like 1, HGNC:17899) is a protein-coding gene on chromosome 3p24.2, encoding NF-kappa-B inhibitor-interacting Ras-like protein 1 (Q9NYS0). Atypical Ras-like protein that acts as a potent regulator of NF-kappa-B activity by preventing the degradation of NF-kappa-B inhibitor beta (NFKBIB) by most signals, explaining why NFKBIB is more resistant to degradation.

Predicted to enable GTPase activating protein binding activity. Predicted to be involved in Ral protein signal transduction. Predicted to act upstream of or within lung alveolus development; regulation of tumor necrosis factor-mediated signaling pathway; and surfactant homeostasis. Located in cytosol and endoplasmic reticulum.

Source: NCBI Gene 28512 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 221 total — 10 pathogenic, 2 likely-pathogenic
• MANE Select transcript: NM_020345

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17899
Approved symbol	NKIRAS1
Name	NFKB inhibitor interacting Ras like 1
Location	3p24.2
Locus type	gene with protein product
Status	Approved
Aliases	KBRAS1, kappaB-Ras1
Ensembl gene	ENSG00000197885
Ensembl biotype	protein_coding
OMIM	604496
Entrez	28512

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 31 protein_coding

ENST00000388759, ENST00000412028, ENST00000415901, ENST00000416026, ENST00000421515, ENST00000425478, ENST00000437230, ENST00000443659, ENST00000614374, ENST00000856683, ENST00000856684, ENST00000856685, ENST00000856686, ENST00000856687, ENST00000856688, ENST00000856689, ENST00000856690, ENST00000856691, ENST00000856692, ENST00000856693, ENST00000856694, ENST00000913300, ENST00000913301, ENST00000913302, ENST00000913303, ENST00000913304, ENST00000941381, ENST00000941382, ENST00000941383, ENST00000941384, ENST00000941385

RefSeq mRNA: 24 — MANE Select: NM_020345 NM_001377351, NM_001377352, NM_001377353, NM_001377354, NM_001377355, NM_001377356, NM_001377357, NM_001377358, NM_001377359, NM_001377360, NM_001377361, NM_001377362, NM_001377363, NM_001377364, NM_001377365, NM_001377366, NM_001377367, NM_001377368, NM_001377369, NM_001377370, NM_001377371, NM_001377372, NM_001377380, NM_020345

CCDS: CCDS33717

Canonical transcript exons

ENST00000425478 — 5 exons

Exon	Start	End
ENSE00001503869	23900808	23901049
ENSE00001503870	23910811	23910921
ENSE00001525947	23911329	23911450
ENSE00001700795	23916784	23916990
ENSE00001856156	23889951	23893337

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 96.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.8152 / max 258.3651, expressed in 1746 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41463	8.2384	1721
41464	0.9782	436
41462	0.5986	306

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lateral nuclear group of thalamus	UBERON:0002736	96.86	gold quality
pons	UBERON:0000988	96.60	gold quality
substantia nigra pars compacta	UBERON:0001965	96.17	gold quality
superior vestibular nucleus	UBERON:0007227	95.49	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.52	gold quality
Brodmann (1909) area 46	UBERON:0006483	94.21	gold quality
prefrontal cortex	UBERON:0000451	94.19	gold quality
lateral globus pallidus	UBERON:0002476	93.98	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.90	gold quality
ventral tegmental area	UBERON:0002691	93.78	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.78	gold quality
vastus lateralis	UBERON:0001379	93.65	gold quality
middle temporal gyrus	UBERON:0002771	93.49	gold quality
superior frontal gyrus	UBERON:0002661	93.30	gold quality
medulla oblongata	UBERON:0001896	93.29	gold quality
frontal cortex	UBERON:0001870	93.01	gold quality
hypothalamus	UBERON:0001898	92.80	gold quality
parietal lobe	UBERON:0001872	92.62	gold quality
neocortex	UBERON:0001950	92.59	gold quality
anterior cingulate cortex	UBERON:0009835	92.45	gold quality
deltoid	UBERON:0001476	92.39	gold quality
cerebral cortex	UBERON:0000956	92.38	gold quality
biceps brachii	UBERON:0001507	92.30	gold quality
dorsal plus ventral thalamus	UBERON:0001897	92.30	gold quality
postcentral gyrus	UBERON:0002581	92.15	gold quality
quadriceps femoris	UBERON:0001377	92.07	gold quality
entorhinal cortex	UBERON:0002728	91.91	gold quality
endothelial cell	CL:0000115	91.64	gold quality
nucleus accumbens	UBERON:0001882	91.62	gold quality
temporal lobe	UBERON:0001871	91.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.91
E-MTAB-6142	no	138.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting NKIRAS1, 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-513A-5P	100.00	69.77	2465
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-466	99.67	70.85	2863

Literature-anchored findings (GeneRIF, showing 5)

• It was shown the decreased expression level of NKIRAS1 in Renal cell carcinoma (PMID:20693965)
• Low kappaB-Ras1 expression is associated with gliomas. (PMID:21302000)
• Significant correlation was found between alterations of methylation status of miR-34b/c, miR-193a and the expression level of NKIRAS1 target gene in the primary lung tumors. (PMID:23156677)
• It was demonstrated that elevated levels of mRNA for NKIRAS1 was significantly associated both with loss of methylation in NKIRAS1 CpG-islands and methylation in a number of miRNA genes. (PMID:25869366)
• A pan-cancer analysis implicates human NKIRAS1 as a tumor-suppressor gene. (PMID:37931099)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nkiras1	ENSDARG00000099527
mus_musculus	Nkiras1	ENSMUSG00000021772
rattus_norvegicus	Nkiras1	ENSRNOG00000008565

Paralogs (35): RALA (ENSG00000006451), REM1 (ENSG00000088320), RASL10A (ENSG00000100276), RASD2 (ENSG00000100302), RASL12 (ENSG00000103710), RHEB (ENSG00000106615), RASD1 (ENSG00000108551), RERGL (ENSG00000111404), RAP1A (ENSG00000116473), RASL11A (ENSG00000122035), RAP2C (ENSG00000123728), RAP2A (ENSG00000125249), RRAS (ENSG00000126458), RAP1B (ENSG00000127314), RASL11B (ENSG00000128045), KRAS (ENSG00000133703), RRAS2 (ENSG00000133818), RERG (ENSG00000134533), REM2 (ENSG00000139890), RIT1 (ENSG00000143622), RALB (ENSG00000144118), RIT2 (ENSG00000152214), MRAS (ENSG00000158186), DIRAS3 (ENSG00000162595), GEM (ENSG00000164949), DIRAS2 (ENSG00000165023), RRAD (ENSG00000166592), RHEBL1 (ENSG00000167550), NKIRAS2 (ENSG00000168256), HRAS (ENSG00000174775), DIRAS1 (ENSG00000176490), RAP2B (ENSG00000181467), ERAS (ENSG00000187682), NRAS (ENSG00000213281), RASL10B (ENSG00000270885)

Protein

Protein identifiers

NF-kappa-B inhibitor-interacting Ras-like protein 1 — Q9NYS0 (reviewed: Q9NYS0)

Alternative names: I-kappa-B-interacting Ras-like protein 1

All UniProt accessions (2): Q9NYS0, G5E9P3

UniProt curated annotations — full annotation on UniProt →

Function. Atypical Ras-like protein that acts as a potent regulator of NF-kappa-B activity by preventing the degradation of NF-kappa-B inhibitor beta (NFKBIB) by most signals, explaining why NFKBIB is more resistant to degradation. May act by blocking phosphorylation of NFKBIB and mediating cytoplasmic retention of p65/RELA NF-kappa-B subunit. It is unclear whether it acts as a GTPase. Both GTP- and GDP-bound forms block phosphorylation of NFKBIB.

Subunit / interactions. Interacts with both NF-kappa-B inhibitor alpha (NFKBIA) and beta (NFKBIB) in vitro. However, it probably only interacts with NFKBIB in vivo. Forms a complex with NFKBIB and NF-kappa-B heterodimer (p50/NFKB1 and p65/RELA). Also interacts with c-Rel (REL).

Subcellular location. Cytoplasm.

Tissue specificity. Widely expressed.

Domain organisation. In contrast to other members of the Ras family, the members of the KappaB-Ras subfamily do not contain the conserved Gly and Gln residues in positions 13 and 65, which are replaced by Leu residues, and are therefore similar to the constitutively active forms of oncogenic forms of Ras. This suggests that members of this family are clearly different from other small GTPases proteins.

Similarity. Belongs to the small GTPase superfamily. Ras family. KappaB-Ras subfamily.

RefSeq proteins (24): NP_001364280, NP_001364281, NP_001364282, NP_001364283, NP_001364284, NP_001364285, NP_001364286, NP_001364287, NP_001364288, NP_001364289, NP_001364290, NP_001364291, NP_001364292, NP_001364293, NP_001364294, NP_001364295, NP_001364296, NP_001364297, NP_001364298, NP_001364299, NP_001364300, NP_001364301, NP_001364309, NP_065078* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001806	Small_GTPase	Family
IPR005225	Small_GTP-bd	Domain
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR042227	KBRS	Family

Pfam: PF00071

UniProt features (9 total): binding site 3, region of interest 2, chain 1, short sequence motif 1, mutagenesis site 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9QU1	X-RAY DIFFRACTION	2.72

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYS0-F1	87.67	0.71

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 (3): 11–18; 61–65; 120–123

Mutagenesis-validated functional residues (1):

Position	Phenotype
38	loss of function.

Function

Pathways and Gene Ontology

Reactome pathways

28 pathways

ID	Pathway
R-HSA-1810476	RIP-mediated NFkB activation via ZBP1
R-HSA-445989	TAK1-dependent IKK and NF-kappa-B activation
R-HSA-933542	TRAF6 mediated NF-kB activation
R-HSA-1280215	Cytokine Signaling in Immune system
R-HSA-1606322	ZBP1(DAI) mediated induction of type I IFNs
R-HSA-166016	Toll Like Receptor 4 (TLR4) Cascade
R-HSA-166058	MyD88:MAL(TIRAP) cascade initiated on plasma membrane
R-HSA-166166	MyD88-independent TLR4 cascade
R-HSA-168138	Toll Like Receptor 9 (TLR9) Cascade
R-HSA-168142	Toll Like Receptor 10 (TLR10) Cascade
R-HSA-168164	Toll Like Receptor 3 (TLR3) Cascade
R-HSA-168176	Toll Like Receptor 5 (TLR5) Cascade
R-HSA-168179	Toll Like Receptor TLR1:TLR2 Cascade
R-HSA-168181	Toll Like Receptor 7/8 (TLR7/8) Cascade
R-HSA-168188	Toll Like Receptor TLR6:TLR2 Cascade
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System
R-HSA-168898	Toll-like Receptor Cascades
R-HSA-168928	DDX58/IFIH1-mediated induction of interferon-alpha/beta
R-HSA-181438	Toll Like Receptor 2 (TLR2) Cascade
R-HSA-1834949	Cytosolic sensors of pathogen-associated DNA
R-HSA-446652	Interleukin-1 family signaling
R-HSA-449147	Signaling by Interleukins
R-HSA-9020702	Interleukin-1 signaling
R-HSA-937061	TRIF (TICAM1)-mediated TLR4 signaling
R-HSA-975138	TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation
R-HSA-975155	MyD88 dependent cascade initiated on endosome
R-HSA-975871	MyD88 cascade initiated on plasma membrane

MSigDB gene sets: 162 (showing top): REACTOME_DDX58_IFIH1_MEDIATED_INDUCTION_OF_INTERFERON_ALPHA_BETA, REACTOME_INNATE_IMMUNE_SYSTEM, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GOBP_RESPONSE_TO_PEPTIDE, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_TUMOR_NECROSIS_FACTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, SANSOM_APC_TARGETS_DN, GOBP_REGULATION_OF_TUMOR_NECROSIS_FACTOR_MEDIATED_SIGNALING_PATHWAY, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, GOBP_RESPIRATORY_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_RESPONSE_TO_CYTOKINE_STIMULUS, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION

GO Biological Process (5): regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803), Ral protein signal transduction (GO:0032484), negative regulation of canonical NF-kappaB signal transduction (GO:0043124), surfactant homeostasis (GO:0043129), lung alveolus development (GO:0048286)

GO Molecular Function (4): GTPase activity (GO:0003924), GTP binding (GO:0005525), GTPase activating protein binding (GO:0032794), nucleotide binding (GO:0000166)

GO Cellular Component (3): endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-16 pathways:

Category	Pathways
Toll-like Receptor Cascades	7
Immune System	2
Toll Like Receptor 4 (TLR4) Cascade	2
Toll Like Receptor 2 (TLR2) Cascade	2
Innate Immune System	2
ZBP1(DAI) mediated induction of type I IFNs	1
MyD88:MAL(TIRAP) cascade initiated on plasma membrane	1
Toll Like Receptor 3 (TLR3) Cascade	1
Interleukin-1 signaling	1
TRIF (TICAM1)-mediated TLR4 signaling	1
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation	1
MyD88 cascade initiated on plasma membrane	1
DDX58/IFIH1-mediated induction of interferon-alpha/beta	1
Cytosolic sensors of pathogen-associated DNA	1
Toll Like Receptor TLR1:TLR2 Cascade	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
cellular anatomical structure	2
regulation of cytokine-mediated signaling pathway	1
tumor necrosis factor-mediated signaling pathway	1
small GTPase-mediated signal transduction	1
canonical NF-kappaB signal transduction	1
regulation of canonical NF-kappaB signal transduction	1
negative regulation of intracellular signal transduction	1
multicellular organismal-level chemical homeostasis	1
lung development	1
anatomical structure development	1
ribonucleoside triphosphate phosphatase activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
protein binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

436 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NKIRAS1	NFKBIB	Q15653	835
NKIRAS1	NFKBIE	O00221	613
NKIRAS1	NFKBIA	P25963	579
NKIRAS1	TEX2	Q8IWB9	456
NKIRAS1	TTC7B	Q86TV6	449
NKIRAS1	LRRC3B	Q96PB8	447
NKIRAS1	RELA	Q04206	410
NKIRAS1	CGGBP1	Q9UFW8	396
NKIRAS1	ATP2B4	P23634	390
NKIRAS1	RANBP1	P43487	389
NKIRAS1	REL	Q04864	388
NKIRAS1	RASL10B	Q96S79	388
NKIRAS1	NDC1	Q9BTX1	377
NKIRAS1	TBCD	Q9BTW9	353
NKIRAS1	CCND1	P24385	351

IntAct

14 interactions, top by confidence:

A	B	Type	Score
ARL4C	RGS12	psi-mi:“MI:0914”(association)	0.640
CBLN4	C1QL1	psi-mi:“MI:0914”(association)	0.530
	NKIRAS1	psi-mi:“MI:0407”(direct interaction)	0.440
NKIRAS1	HSPD1	psi-mi:“MI:0915”(physical association)	0.400
NKIRAS1	XRCC2	psi-mi:“MI:0915”(physical association)	0.370
SLAMF1	RTCA	psi-mi:“MI:0914”(association)	0.350
CBLN4	ADAM11	psi-mi:“MI:0914”(association)	0.350
PAEP	RTCA	psi-mi:“MI:0914”(association)	0.350
CCT8L2	DVL2	psi-mi:“MI:0914”(association)	0.350
LCN9	C1QL1	psi-mi:“MI:0914”(association)	0.350
NAA30	HARS2	psi-mi:“MI:0914”(association)	0.350
MAGT1	TUBA4A	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NFKBIB (Affinity Capture-Western), NKIRAS1 (Affinity Capture-RNA), NKIRAS1 (Proximity Label-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-MS), NKIRAS1 (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: O15294, O89050, O95057, P11233, P22124, P35290, P36860, P56558, P63320, P63321, P63322, P79101, P81436, Q03555, Q05048, Q27HV0, Q5BJQ6, Q5EA19, Q5NVN7, Q5PR73, Q5R4Q7, Q5R6S2, Q5R8K2, Q5RB35, Q5RFN0, Q5RKN4, Q5ZJW6, Q8BGR6, Q8BUV3, Q8CEC5, Q8CGY8, Q8N653, Q91Z61, Q95KD9, Q969Q5, Q96HU8, Q96NJ5, Q99LC2, Q99PV3, Q9BH04

Diamond homologs: A5A6J7, A6NIZ1, C4YKT4, E9R5S0, O35626, P01119, P0CY32, P11234, P13856, P18613, P22123, P22279, P36860, P52498, P61223, P61224, P62833, P62834, P62835, P62836, P79737, Q18246, Q19143, Q32NS2, Q4R379, Q4R9D4, Q4X241, Q550Q4, Q55BW0, Q59XU5, Q5R4B8, Q5RDM6, Q5ZHX1, Q5ZJW6, Q62636, Q640R7, Q6DGL2, Q6DGQ1, Q6IP71, Q6TEN1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	10
Likely pathogenic	2
Uncertain significance	101
Likely benign	65
Benign	18

Top pathogenic / likely-pathogenic (12)

Variant ID	HGVS	Classification
1380966	NM_002948.5(RPL15):c.211C>T (p.Arg71Ter)	Pathogenic
1709989	NM_002948.5(RPL15):c.130del (p.Arg44fs)	Pathogenic
2502335	NM_002948.5(RPL15):c.242dup (p.Tyr81Ter)	Pathogenic
2502336	NM_002948.5(RPL15):c.85C>T (p.Gln29Ter)	Pathogenic
2502337	NM_002948.5(RPL15):c.29T>C (p.Leu10Pro)	Pathogenic
2502338	NM_002948.5(RPL15):c.458A>C (p.Lys153Thr)	Pathogenic
2672935	NM_002948.5(RPL15):c.165_172+16del	Pathogenic
280195	NM_002948.5(RPL15):c.310-2A>G	Pathogenic
4282374	NM_002948.5(RPL15):c.243C>G (p.Tyr81Ter)	Pathogenic
88980	NM_001253384.2(RPL15):c.309+91_361-539del	Pathogenic
3907760	NM_002948.5(RPL15):c.313C>T (p.Arg105Ter)	Likely pathogenic
870411	NM_002948.5(RPL15):c.314G>T (p.Arg105Leu)	Likely pathogenic

SpliceAI

2238 predictions. Top by Δscore:

Variant	Effect	Δscore
3:23900830:T:C	donor_gain	1.0000
3:23900944:T:TA	donor_gain	1.0000
3:23902884:A:AC	donor_gain	1.0000
3:23902885:C:CC	donor_gain	1.0000
3:23910805:TCTTA:T	donor_loss	1.0000
3:23910806:CTTA:C	donor_loss	1.0000
3:23910807:TTA:T	donor_loss	1.0000
3:23910808:TA:T	donor_loss	1.0000
3:23910810:C:T	donor_loss	1.0000
3:23910917:TATCA:T	acceptor_gain	1.0000
3:23910918:ATCA:A	acceptor_gain	1.0000
3:23910919:TCA:T	acceptor_gain	1.0000
3:23910920:CA:C	acceptor_gain	1.0000
3:23910920:CAC:C	acceptor_gain	1.0000
3:23910922:C:CC	acceptor_gain	1.0000
3:23917089:A:T	donor_gain	1.0000
3:23918027:GCAAG:G	donor_gain	1.0000
3:23918029:AAGG:A	donor_loss	1.0000
3:23918030:AGGT:A	donor_loss	1.0000
3:23918031:GGT:G	donor_loss	1.0000
3:23918032:G:C	donor_loss	1.0000
3:23918435:T:TA	acceptor_gain	1.0000
3:23918438:A:AG	acceptor_gain	1.0000
3:23918438:AG:A	acceptor_gain	1.0000
3:23918439:G:GG	acceptor_gain	1.0000
3:23918439:GG:G	acceptor_gain	1.0000
3:23918439:GGT:G	acceptor_gain	1.0000
3:23918439:GGTT:G	acceptor_gain	1.0000
3:23918439:GGTTA:G	acceptor_gain	1.0000
3:23918541:C:G	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000005534 (3:23912837 C>A,T), RS1000011300 (3:23897598 C>T), RS1000066365 (3:23946154 G>A,T), RS1000161174 (3:23910047 C>T), RS1000266795 (3:23943828 G>A), RS1000387932 (3:23916005 T>C), RS1000397903 (3:23938909 T>C,G), RS1000436754 (3:23916207 T>C,G), RS1000448866 (3:23938536 G>A), RS1000451607 (3:23909130 T>C), RS1000459583 (3:23891120 T>C), RS1000483359 (3:23901538 C>T), RS1000501782 (3:23909314 G>A), RS1000587334 (3:23933236 G>C), RS1000589991 (3:23932953 A>G)

Disease associations

OMIM: gene MIM:604496 | disease phenotypes: MIM:615550

GenCC curated gene-disease

Mondo (1): Diamond-Blackfan anemia 12 (MONDO:0014245)

Orphanet (1): Diamond-Blackfan anemia (Orphanet:124)

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002481_10	Acne (severe)	1.000000e-06
GCST005316_102	Intelligence (MTAG)	4.000000e-08
GCST005316_103	Intelligence (MTAG)	2.000000e-15
GCST005316_291	Intelligence (MTAG)	2.000000e-11
GCST006269_311	General cognitive ability	7.000000e-12
GCST006269_622	General cognitive ability	1.000000e-13
GCST007044_10	Extremely high intelligence	3.000000e-11
GCST008759_44	Intake of total sugars	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0010158	sugar consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression, affects expression	3
sodium arsenite	increases abundance, increases expression	2
GSK-J4	increases expression	1
2-anisidine	affects expression	1
beta-methylcholine	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Temozolomide	increases expression	1
Arsenic	increases expression, increases abundance	1
Doxorubicin	decreases expression	1
Fluorouracil	affects expression	1
Formaldehyde	decreases expression	1
Lead	affects expression	1
Methyl Methanesulfonate	decreases expression	1
Phenobarbital	affects expression	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	increases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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