HOXB5

Summary

HOXB5 (homeobox B5, HGNC:5116) is a protein-coding gene on chromosome 17q21.32, encoding Homeobox protein Hox-B5 (P09067). Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in lung and gut development. Increased expression of this gene is associated with a distinct biologic subset of acute myeloid leukemia (AML) and the occurrence of bronchopulmonary sequestration (BPS) and congenital cystic adenomatoid malformation (CCAM) tissue.

Source: NCBI Gene 3215 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• MANE Select transcript: NM_002147

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:5116
Approved symbol	HOXB5
Name	homeobox B5
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000120075
Ensembl biotype	protein_coding
OMIM	142960
Entrez	3215

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000239151

RefSeq mRNA: 1 — MANE Select: NM_002147 NM_002147

CCDS: CCDS11530

Canonical transcript exons

ENST00000239151 — 2 exons

Exon	Start	End
ENSE00000812637	48591257	48592456
ENSE00000812638	48593121	48593779

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 89.10.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7160 / max 227.3442, expressed in 387 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166693	0.5927	189
166690	0.3286	138
166692	0.2901	130
166691	0.1675	72
166689	0.1413	61
166685	0.0728	35
166694	0.0723	35
166684	0.0509	21

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	89.10	gold quality
ileal mucosa	UBERON:0000331	85.46	gold quality
metanephros cortex	UBERON:0010533	85.26	gold quality
corpus epididymis	UBERON:0004359	84.31	gold quality
pancreatic ductal cell	CL:0002079	84.27	gold quality
transverse colon	UBERON:0001157	84.24	gold quality
cervix squamous epithelium	UBERON:0006922	83.30	silver quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	83.15	gold quality
small intestine Peyer’s patch	UBERON:0003454	80.51	gold quality
triceps brachii	UBERON:0001509	79.67	gold quality
gluteal muscle	UBERON:0002000	79.42	gold quality
colon	UBERON:0001155	78.98	gold quality
large intestine	UBERON:0000059	78.80	gold quality
adult mammalian kidney	UBERON:0000082	78.58	gold quality
endometrium	UBERON:0001295	78.21	gold quality
intestine	UBERON:0000160	78.11	gold quality
seminal vesicle	UBERON:0000998	77.91	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.90	gold quality
inferior olivary complex	UBERON:0002127	77.77	gold quality
small intestine	UBERON:0002108	77.74	gold quality
caput epididymis	UBERON:0004358	77.43	gold quality
sigmoid colon	UBERON:0001159	77.36	gold quality
metanephros	UBERON:0000081	76.96	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.82	gold quality
tendon of biceps brachii	UBERON:0008188	76.72	gold quality
right lung	UBERON:0002167	76.45	gold quality
right uterine tube	UBERON:0001302	76.33	gold quality
kidney	UBERON:0002113	76.28	gold quality
spinal cord	UBERON:0002240	76.13	gold quality
mucosa of stomach	UBERON:0001199	75.89	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-10485	yes	1352.55
E-CURD-114	yes	12.24
E-ANND-3	yes	5.64

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

Target	Regulation
ANGPT2
KDR	Activation
RASSF1
RET
TNC	Unknown

JASPAR motifs

Motif	Name	Family
MA0904.2	HOXB5	HOX
MA0904.3	HOXB5	HOX

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): ARID4B

miRNA regulators (miRDB)

82 targeting HOXB5, 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-5692A	100.00	74.40	6850
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-539-5P	99.93	70.30	2855

Literature-anchored findings (GeneRIF, showing 25)

• HoxB5 is necessary and sufficient to activate the cell-intrinsic events that regulate the differentiation of angioblasts and mature endothelial cells from their mesoderm-derived precursors (PMID:12897140)
• The expression pattern of HOXB5 correlated with the migration and differentiation of neural crest cells. (PMID:12950074)
• DNA hypermethylation of tumour suppressor genes seems to play an important role in ovarian carcinogenesis and HOXA9, HOXB5, SCGB3A1, and CRABP1 are identified as novel hypermethylated target genes in this tumour type (PMID:17623056)
• results support that expression of HOX genes is associated with oral squamous cell carcinoma; over 90% of OSCC samples presented HOXB5 expression versus 60% of non-tumor tissues, it can be suggested that HOXB5 may be related to the malignant phenotypes. (PMID:21552713)
• Data show that human HOXB5 binds to the promoter region 5’ upstream of the binding site of NKX2-1 and regulates RET expression. (PMID:21677782)
• Single nucleotide polymorphism in HOXB5 gene is associated with childhood obesity. (PMID:22484627)
• HOXB5, HOXB6, and HOXB7 are activated in Barrett esophagus, and the midcluster HOXB gene signature in BE most resembled the colon rather than other GI epithelia. (PMID:22603795)
• The findings for HOXB5 and PHOX2B provide supportive evidence that genes regulating ENCC proliferation, migration and differentiation could be risk factors for Hirschsprung’s disease (PMID:22648184)
• A miRNA 7-binding single nucleotide polymorphism (1010A/G) located within 3’-UTR of HOXB5 is associated with gene expression and may be a promising prognostic factor for bladder cancer. (PMID:22768238)
• HOXB5 and HOXB8 are frequently expressed in ovarian serous carcinoma, with anatomic site-related differences for cytoplasmic staining. HOXB5 may be affected by chemotherapy in effusions. (PMID:23438671)
• Overexpression of HoxB5 enhances blood vessel perfusion in vivo by up-regulation of MCP-1 and IL-6 as well as in enhanced leucocyte infiltration and blood vessel remodelling. (PMID:24189625)
• Roles of Hoxb5 in the development of vagal and trunk neural crest cells. (PMID:25703667)
• HOXB5 acts as a positive modulator by promoting cell proliferative response and invasiveness in ER-positive breast cancer. (PMID:25999793)
• HOXB5 may be an important regulator of the Wnt/beta-catenin signalling pathway, thereby contributing to gastric cancer progression and metastasis. (PMID:26467157)
• for the first time we have shown that knockdown of HOXB5 significantly inhibited non-small cell lung cancer cell proliferation, invasion, metastasis, and epithelial-mesenchymal transformation, partly through the Wnt/beta-catenin signaling pathway (PMID:28337958)
• Taken together, our results for the first time suggested that miR-455-3p was downregulated in NSCLC and was correlated with the poor prognosis of NSCLC patients. Also, miR-455-3p functions as tumor suppressor by directly targeting HOXB5 in NSCLC progression and may be used as a potential target for NSCLC treatment. (PMID:29170127)
• In breast cancer cells, HOXB5 regulates EGFR expression at the transcriptional level by directly binding to its promoter region and promotes phosphorylation of EGFR as well as its downstream effectors (PMID:30115380)
• HOXB5 acts as an oncogenic driver in head and neck squamous cell carcinoma via EGFR/Akt/Wnt/beta-catenin signaling axis. (PMID:31864826)
• HOXB5 promotes malignant progression in pancreatic cancer via the miR-6732 pathway. (PMID:31876226)
• Homeobox B5 suppression attenuates proliferation and elevates apoptosis in hepatoma cell lines through ERK/MDM2 signalling. (PMID:32037602)
• HOXB5 promotes proliferation, migration, and invasion of pancreatic cancer cell through the activation of the GSK3beta/beta-catenin pathway. (PMID:32796404)
• CXCL12-mediated HOXB5 overexpression facilitates Colorectal Cancer metastasis through transactivating CXCR4 and ITGB3. (PMID:33456563)
• HOXB5 promotes the progression of breast cancer through wnt/beta-catenin pathway. (PMID:34118725)
• HOXB5 Confers Tamoxifen Resistance in Breast Cancer Cells and Promotes Tumor Aggression and Progression. (PMID:34230136)
• Circ_0020123 enhances the cisplatin resistance in non-small cell lung cancer cells partly by sponging miR-140-3p to regulate homeobox B5 (HOXB5). (PMID:35170372)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	hoxb5a	ENSDARG00000013057
danio_rerio	hoxb5b	ENSDARG00000054030
mus_musculus	Hoxb5	ENSMUSG00000038700
rattus_norvegicus		ENSRNOG00000081481

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC11 (ENSG00000123388), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-B5 — P09067 (reviewed: P09067)

Alternative names: Homeobox protein HHO.C10, Homeobox protein Hox-2A, Homeobox protein Hu-1

All UniProt accessions (1): P09067

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Subcellular location. Nucleus.

Tissue specificity. Spinal cord.

Similarity. Belongs to the Antp homeobox family.

RefSeq proteins (1): NP_002138* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR001827	Homeobox_Antennapedia_CS	Conserved_site
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR017995	Homeobox_antennapedia	Family
IPR020479	HD_metazoa	Domain
IPR050296	Antp_homeobox	Family

Pfam: PF00046

UniProt features (8 total): compositionally biased region 4, chain 1, DNA-binding region 1, region of interest 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P09067-F1	63.38	0.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 203 (showing top): VALK_AML_WITH_FLT3_ITD, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, MULLIGHAN_NPM1_SIGNATURE_3_UP, TAATAAT_MIR126, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, TTTGTAG_MIR520D, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, AP4_Q6, RACCACAR_AML_Q6, TGACCTY_ERR1_Q2

GO Biological Process (8): regulation of transcription by RNA polymerase II (GO:0006357), anatomical structure morphogenesis (GO:0009653), anterior/posterior pattern specification (GO:0009952), endothelial cell differentiation (GO:0045446), embryonic skeletal system morphogenesis (GO:0048704), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944), embryonic skeletal system development (GO:0048706)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), fibrillar center (GO:0001650), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
developmental process	1
anatomical structure development	1
regionalization	1
endothelium development	1
epithelial cell differentiation	1
embryonic organ morphogenesis	1
skeletal system morphogenesis	1
embryonic skeletal system development	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	1
skeletal system development	1
chordate embryonic development	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
chromosome	1
nucleolus	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

1148 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HOXB5	PBX1	P40424	625
HOXB5	RPS16	P17008	590
HOXB5	RPL13A	P40429	553
HOXB5	HOXD8	P13378	545
HOXB5	HOXC9	P31274	527
HOXB5	HOXD9	P28356	517
HOXB5	HOXB9	P17482	513
HOXB5	NGFR	P08138	470
HOXB5	CTNNAL1	Q9UBT7	461
HOXB5	PAX1	P15863	455
HOXB5	MEIS1	O00470	442
HOXB5	ITGA2B	P08514	432
HOXB5	PEBP1	P30086	423
HOXB5	RPS20	P17075	411
HOXB5	FGD5	Q6ZNL6	404

IntAct

200 interactions, top by confidence:

A	B	Type	Score
TRIM23	HOXB5	psi-mi:“MI:0915”(physical association)	0.720
HOXB5	CTBP2	psi-mi:“MI:0915”(physical association)	0.720
HOXB5	TRIM23	psi-mi:“MI:0915”(physical association)	0.720
HOXB5	SIRT1	psi-mi:“MI:0915”(physical association)	0.620
MAGEA11	HOXB5	psi-mi:“MI:0915”(physical association)	0.560
CTBP1	HOXB5	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	MAGEA11	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	CTBP1	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	PHF19	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	VPS52	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	PBX2	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	KRTAP1-1	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	TEKT4	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	HOMER3	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	TRAF2	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	KIFAP3	psi-mi:“MI:0915”(physical association)	0.560
KRT34	HOXB5	psi-mi:“MI:0915”(physical association)	0.560
CADPS	HOXB5	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	TRIM54	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	TRIM27	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	MID2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (160): HOXB5 (Two-hybrid), HOXB5 (Two-hybrid), HOXB5 (Two-hybrid), MAGEA11 (Two-hybrid), PALM (Affinity Capture-MS), PAG1 (Affinity Capture-MS), SMPDL3B (Affinity Capture-MS), ACTB (Affinity Capture-MS), NUP155 (Affinity Capture-MS), GNAO1 (Affinity Capture-MS), GNAQ (Affinity Capture-MS), GNA11 (Affinity Capture-MS), ATP6V0A2 (Affinity Capture-MS), ATP6V0A1 (Affinity Capture-MS), NUP35 (Affinity Capture-MS)

ESM2 similar proteins: A1YEY5, A1YFA5, A1YFI3, A1YG57, A1YGK7, A2D5K9, A2D5Y4, A2T733, A2T748, A2T7F3, A2T7P4, O95096, P02830, P04476, P09021, P09024, P09067, P09629, P09631, P18864, P20719, P23459, P23463, P31268, P31269, P35453, P42586, P43697, P56915, P70217, P81068, P97334, Q02591, Q1KKX0, Q1KKX1, Q1KKY0, Q1KKY1, Q1KL17, Q2HJ67, Q5EU41

Diamond homologs: A1L2P5, A1YER7, A1YF08, A1YFD8, A1YFY3, A1YG85, A2D4P8, A2D5I1, A2D5K9, A2D5Y4, A2T6X6, A2T756, A8DT10, A9L937, B0VXK3, O13074, O42365, O42367, O42368, O42370, O43364, O43365, O57374, O93353, P02830, P02831, P06798, P09013, P09014, P09016, P09019, P09020, P09021, P09026, P09027, P09067, P09070, P09074, P09079, P09080

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 63 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
Repression of WNT target genes	5	96.5×	2e-07
Keratinization	6	9.0×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

97 predictions. Top by Δscore:

Variant	Effect	Δscore
17:48592452:CATAT:C	acceptor_gain	1.0000
17:48592453:ATAT:A	acceptor_gain	1.0000
17:48592454:TAT:T	acceptor_gain	1.0000
17:48592455:AT:A	acceptor_gain	1.0000
17:48592456:TCTGG:T	acceptor_loss	1.0000
17:48592457:C:CA	acceptor_loss	1.0000
17:48592457:C:CC	acceptor_gain	1.0000
17:48592463:CAGA:C	acceptor_gain	1.0000
17:48592464:A:T	acceptor_gain	1.0000
17:48592466:A:AC	acceptor_gain	1.0000
17:48592466:A:C	acceptor_gain	1.0000
17:48592478:C:CT	acceptor_gain	1.0000
17:48593116:ATTAC:A	donor_loss	1.0000
17:48593117:TTAC:T	donor_loss	1.0000
17:48593118:TA:T	donor_loss	1.0000
17:48593119:A:AC	donor_gain	1.0000
17:48593120:C:CC	donor_gain	1.0000
17:48593120:C:CT	donor_loss	1.0000
17:48593139:T:TA	donor_gain	1.0000
17:48592478:C:T	acceptor_gain	0.9900
17:48593238:G:C	donor_gain	0.9900
17:48593119:AC:A	donor_gain	0.9800
17:48593120:CC:C	donor_gain	0.9800
17:48593252:T:TA	donor_gain	0.9700
17:48593120:CCATG:C	donor_gain	0.9600
17:48593120:CCA:C	donor_gain	0.9400
17:48592453:ATATC:A	acceptor_gain	0.9300
17:48592454:TATC:T	acceptor_gain	0.9300
17:48592455:ATC:A	acceptor_gain	0.9300
17:48592456:TCT:T	acceptor_gain	0.9300

AlphaMissense

1771 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:48592266:C:A	K251N	1.000
17:48592266:C:G	K251N	1.000
17:48592267:T:A	K251M	1.000
17:48592268:T:C	K251E	1.000
17:48592269:C:A	K250N	1.000
17:48592269:C:G	K250N	1.000
17:48592270:T:A	K250M	1.000
17:48592270:T:G	K250T	1.000
17:48592271:T:C	K250E	1.000
17:48592274:A:G	W249R	1.000
17:48592274:A:T	W249R	1.000
17:48592275:C:A	K248N	1.000
17:48592275:C:G	K248N	1.000
17:48592276:T:A	K248M	1.000
17:48592277:T:C	K248E	1.000
17:48592278:C:A	M247I	1.000
17:48592278:C:G	M247I	1.000
17:48592278:C:T	M247I	1.000
17:48592279:A:C	M247R	1.000
17:48592279:A:G	M247T	1.000
17:48592279:A:T	M247K	1.000
17:48592282:C:G	R246P	1.000
17:48592282:C:T	R246H	1.000
17:48592283:G:A	R246C	1.000
17:48592283:G:C	R246G	1.000
17:48592283:G:T	R246S	1.000
17:48592285:C:A	R245L	1.000
17:48592285:C:G	R245P	1.000
17:48592286:G:A	R245W	1.000
17:48592286:G:C	R245G	1.000

dbSNP variants (sampled 300 via entrez): RS1000350690 (17:48592590 C>G), RS1000370770 (17:48593445 C>T), RS1000781882 (17:48594727 G>C), RS1000829001 (17:48591226 C>A,G), RS1000845993 (17:48592949 G>A), RS1001110795 (17:48595092 C>A,G), RS1002283412 (17:48594156 G>C,T), RS1002616517 (17:48594525 C>A,G), RS1002835826 (17:48591263 G>A,T), RS1002910787 (17:48590999 C>T), RS1003172286 (17:48592830 G>T), RS1003703994 (17:48595603 C>T), RS1004221300 (17:48593741 C>A,G), RS1004566000 (17:48595429 G>A), RS1004594421 (17:48594116 C>T)

Disease associations

OMIM: gene MIM:142960 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001475_2	Obesity	4.000000e-09
GCST006479_8	Diverticular disease	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009959	diverticular disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tretinoin	affects reaction, increases expression, affects cotreatment	4
bisphenol A	decreases expression, affects cotreatment, increases expression	2
bisphenol S	decreases methylation, affects cotreatment, decreases expression	2
Nickel	decreases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
aristolochic acid I	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases methylation	1
butyraldehyde	decreases expression	1
sodium tungstate(VI)	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects reaction	1
Chir 99021	affects reaction, increases expression	1
ICG 001	increases expression	1
abrine	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic	increases methylation	1
Curcumin	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	decreases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Triclosan	increases expression	1
Tunicamycin	decreases expression	1
Valproic Acid	affects expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Asbestos, Crocidolite	decreases methylation	1
Asbestos, Amosite	decreases methylation	1

Clinical trials (associated diseases)

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