HBP1

Summary

HBP1 (HMG-box transcription factor 1, HGNC:23200) is a protein-coding gene on chromosome 7q22.3, encoding HMG box-containing protein 1 (O60381). Transcriptional repressor that binds to the promoter region of target genes.

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of lipid transport; negative regulation of reactive oxygen species biosynthetic process; and negative regulation of transcription by RNA polymerase II. Located in nuclear speck. Biomarker of osteoarthritis.

Source: NCBI Gene 26959 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 72 total
• Transcription factor: yes — 51 downstream targets (CollecTRI)
• MANE Select transcript: NM_012257

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23200
Approved symbol	HBP1
Name	HMG-box transcription factor 1
Location	7q22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000105856
Ensembl biotype	protein_coding
OMIM	616714
Entrez	26959

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 34 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000222574, ENST00000461963, ENST00000463202, ENST00000463790, ENST00000464009, ENST00000468116, ENST00000468401, ENST00000468410, ENST00000478930, ENST00000479011, ENST00000483809, ENST00000485846, ENST00000497535, ENST00000498408, ENST00000607681, ENST00000895657, ENST00000895658, ENST00000895659, ENST00000895660, ENST00000895661, ENST00000895662, ENST00000895663, ENST00000895664, ENST00000895669, ENST00000895670, ENST00000938515, ENST00000938516, ENST00000938517, ENST00000938518, ENST00000938519, ENST00000958454, ENST00000958455, ENST00000958456, ENST00000958457, ENST00000958458, ENST00000958459, ENST00000958460, ENST00000958461, ENST00000958462

RefSeq mRNA: 2 — MANE Select: NM_012257 NM_001244262, NM_012257

CCDS: CCDS5741

Canonical transcript exons

ENST00000222574 — 11 exons

Exon	Start	End
ENSE00000881751	107179879	107180062
ENSE00001374924	107169003	107169185
ENSE00001829379	107201414	107202522
ENSE00003471514	107200160	107200301
ENSE00003484360	107189292	107189448
ENSE00003501829	107185801	107185942
ENSE00003533154	107195834	107196151
ENSE00003545334	107182373	107182601
ENSE00003576618	107186361	107186472
ENSE00003651458	107190173	107190317
ENSE00003656548	107186569	107186681

Expression profiles

Bgee: expression breadth ubiquitous, 186 present calls, max score 99.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.1998 / max 488.4674, expressed in 1802 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80437	22.3803	1800
80438	1.4065	489
80442	0.6078	196
80441	0.6061	141
80439	0.1034	33
80440	0.0957	30

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	99.12	gold quality
adrenal tissue	UBERON:0018303	98.12	gold quality
right lung	UBERON:0002167	97.23	gold quality
skin of leg	UBERON:0001511	96.91	gold quality
skin of abdomen	UBERON:0001416	96.68	gold quality
bone marrow cell	CL:0002092	96.63	gold quality
tibial artery	UBERON:0007610	96.62	gold quality
popliteal artery	UBERON:0002250	96.61	gold quality
left testis	UBERON:0004533	96.55	gold quality
left ovary	UBERON:0002119	96.53	gold quality
mucosa of stomach	UBERON:0001199	96.50	gold quality
right testis	UBERON:0004534	96.47	gold quality
descending thoracic aorta	UBERON:0002345	96.42	gold quality
ectocervix	UBERON:0012249	96.23	gold quality
gastrocnemius	UBERON:0001388	96.11	gold quality
endocervix	UBERON:0000458	96.10	gold quality
body of uterus	UBERON:0009853	96.10	gold quality
muscle of leg	UBERON:0001383	96.03	gold quality
lower esophagus mucosa	UBERON:0035834	95.93	gold quality
right adrenal gland cortex	UBERON:0035827	95.92	gold quality
aorta	UBERON:0000947	95.79	gold quality
minor salivary gland	UBERON:0001830	95.61	gold quality
right adrenal gland	UBERON:0001233	95.57	gold quality
ventricular zone	UBERON:0003053	95.52	gold quality
right ovary	UBERON:0002118	95.51	gold quality
gall bladder	UBERON:0002110	95.48	gold quality
stromal cell of endometrium	CL:0002255	95.46	gold quality
tibial nerve	UBERON:0001323	95.34	gold quality
right coronary artery	UBERON:0001625	95.32	gold quality
left adrenal gland	UBERON:0001234	95.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	5.84
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

51 targets.

Target	Regulation
BAX
BCL2
BECN1
BMP2
BTG1
CCND1	Repression
CCND3	Repression
CCNE1	Repression
CD74
CDKN1A	Repression
CDKN2A	Activation
CEBPA	Activation
CNTN2
COL2A1
CREBBP
DNMT1	Repression
FASLG	Activation
GATA1	Activation
H1-0	Activation
H1-2
H1-5	Activation
HBP1
HMGB1
IFNAR1
IL1B
IL2
IRS1
JUNB	Activation
MAP1LC3A
MAPK14

Upstream regulators (CollecTRI, top): FOXO3, HBP1, MYC, RB1, TP63

miRNA regulators (miRDB)

123 targeting HBP1, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-126-5P	100.00	72.71	3180
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-767-5P	99.95	70.85	993
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-3910	99.95	71.13	2227
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856

Literature-anchored findings (GeneRIF, showing 40)

• HBP1 regulates the cell cycle in liver regeneration and provides evidence for a role in tissue maintenance. (PMID:11486012)
• HBP1 is a suppressor of Wnt signalling and lies in a region that is mutated in cancer. (PMID:11500377)
• NMR study of the AXH domain (PMID:14872137)
• Results indicate that HBP1 may contribute to the regulation of NADPH oxidase-dependent superoxide production through transcriptional repression of the p47phox gene. (PMID:15024088)
• HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations (PMID:15235594)
• in myeloid cells HBP1 may serve as a tumor suppressor and a general differentiation inducer and may synergize with chemical differentiating agents to enhance lineage-specific differentiation (PMID:16179914)
• Transgenic mice overexpressing HBP1 exhibit altered thymus cellularity and decreased thymocyte development. (PMID:16210625)
• EGCG blocks Wnt signaling by inducing the HBP1 transcriptional repressor and inhibits aspects of invasive breast cancer (PMID:16495219)
• these studies highlight p38 MAPK, HBP1, and RB as important components for a premature-senescence pathway with possible clinical relevance to breast cancer. (PMID:16966377)
• HBP1 transcriptional repressor alterations are associated with invasive breast cancer (PMID:17616670)
• HBP1 binds c-Myc in cells, and expression of HBP1 inhibits c-Myc transactivational activity at least partly by preventing c-Myc binding to target gene promoters. (PMID:20008325)
• HBP1 directly inhibits MIF gene transcription, which is overexpressed in prostatic cancer. (PMID:20383199)
• miR-17-5p plays an important role in breast cancer cell invasion and migration by suppressing HBP1 and subsequent activation of Wnt/beta-catenin (PMID:20505989)
• HBP1 targets P16(INK4A), upregulating its expression and consequently is involved in Ras-induced premature senescence. (PMID:20581871)
• Cis-acting regulatory polymorphisms acting on HBP1 contribute to the osteoarthritis association signal at chromosome 7q22. (PMID:22586168)
• HBP1 represses the DNMT1 gene through binding a high-affinity site in the DNMT1 promoter. (PMID:23249948)
• acetylation of TCF4E is a novel regulatory mechanism that diversifies the transcriptional output of Wnt/beta-catenin signaling (PMID:23613959)
• HBP1 is a novel target of the PI3K/FOXO pathway and controls cell proliferation in response to growth factors. (PMID:24762137)
• HBP1 is a suppressor of cancer progression and a regulator of CTNNB1 gene transcription. (PMID:24895061)
• HBP1-mediated Wnt signaling is involved with the role of miR-155 in osteosarcoma progression. (PMID:25666090)
• Hbp1 plays a crucial role in regulating the timing of cortical neurogenesis by elongating the cell cycle and that it is essential for normal cortical development. (PMID:26041766)
• All trans-retinoic acid can reverse the suppressive effect of MED28 on HBP1 and E-cadherin and inactivate the Wnt/beta-catenin pathway in colorectal cancer, suggesting a protective effect of ATRA against colorectal cancer. (PMID:26660958)
• Data suggest HMG-box transcription factor (HBP1) as a target in prostate cancer radiotherapy. (PMID:26942107)
• Data show that HMG-box transcription factor 1 protein HBP1-mediated elevation of CDK inhibitor p21 through the Mdm2/p53 and TCF4/EZH2 pathways contributes to both cellular senescence and tumor inhibition. (PMID:27129219)
• Low HBP1 expression is associated with invasive oral cancer. (PMID:28099936)
• Study shows that RORbeta is a transcriptional enhancer of inhibitor HBP1 of the Wnt pathway. NRIP2 prevents RORbeta to bind with downstream HBP1 promoter regions and reduces the transcription of HBP1. These results provide evidence that interactions between NRIP2, RORbeta, and HBP1 mediate a new mechanism for CCIC self-renewal via the Wnt activity. (PMID:28137278)
• induced premature senescence and apoptosis. Furthermore, the Pim-1-HBP1 positive feedback loop exerts its effect by regulating the senescence markers DNMT1 and p16 and the apoptosis marker Bax. The Pim-1-HBP1 axis thus constitutes a novel checkpoint pathway critical for the inhibition of tumorigenesis. (PMID:28348080)
• results suggest that HBP1 phosphorylation by AKT blocks its functions as transcriptional regulator and tumor suppressor. (PMID:29355710)
• HBP1 functions as a non-tumor suppressor gene in nasopharyngeal carcinoma. (PMID:29367693)
• Our experiment also verified the target relationship between miR-21 and HBP1. MiR-21 may affect migration and invasion ability of drug-resistant lung adenocarcinoma cells by targeting HBP1, therefore modulating EMT. (PMID:29663730)
• Data show that the GID/CTLH E3 ubiquitin ligase prevents cell cycle exit in G1, at least in part by degrading HMG-box transcription factor 1 protein (Hbp1). (PMID:29911972)
• Reduced HBP1 expression and subsequent MMP-13 upregulation may play a pivotal role in the invasiveness of oral cancer. (PMID:30191992)
• Mutant ALK downregulates the ‘HMG-box transcription factor 1’ (HBP1). (PMID:30538293)
• this review discusses our current understanding of HBP1 function in human physiology and diseases. [Review] (PMID:30683982)
• MDM2 facilitates HBP1 proteasomal degradation by ubiquitinating HBP1, regardless of p53 status, thus attenuating the transcriptional inhibition of HBP1 in the expression of its target genes, such as the DNA methyltransferase DNMT1 and histone methyltransferase EZH2, which results in global DNA hypermethylation and histone hypermethylation and ultimately genome instability. (PMID:30816344)
• HBP1 functions as a tumor suppressor, and its ectopic expression hindered cell proliferation of non-small-cell lung cancer (NSCLC). AFAP1-AS1 repressed HBP1 expression by recruiting LSD1 to the HBP1 promoter regions in NSCLC cell lines. (PMID:31069893)
• Suppression of p38/HBP1 pathway alleviates hyperosmotic stress-induced senescent progression of chondrocyte senescence. (PMID:32549582)
• Regulatory role of transcription factor HBP1 in anticancer efficacy of EGFR inhibitor erlotinib in HNSCC. (PMID:32677158)
• HBP1 deficiency protects against stress-induced premature senescence of nucleus pulposus. (PMID:32964956)
• miR-146b Functions as an Oncogene in Oral Squamous Cell Carcinoma by Targeting HBP1. (PMID:33327874)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	hbp1	ENSDARG00000028517
mus_musculus	Hbp1	ENSMUSG00000002996
rattus_norvegicus	Hbp1	ENSRNOG00000008927

Protein

Protein identifiers

HMG box-containing protein 1 — O60381 (reviewed: O60381)

Alternative names: HMG box transcription factor 1, High mobility group box transcription factor 1

All UniProt accessions (9): O60381, C9J5U3, C9J8V6, C9JAW1, C9JPK6, C9JQU7, H7C4S2, H7C574, U3KQE5

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor that binds to the promoter region of target genes. Plays a role in the regulation of the cell cycle and of the Wnt pathway. Binds preferentially to the sequence 5’-TTCATTCATTCA-3’. Binding to the histone H1.0 promoter is enhanced by interaction with RB1. Disrupts the interaction between DNA and TCF4.

Subunit / interactions. Binds the second PAH repeat of SIN3A. Binds TCF4. Binds RB1.

Subcellular location. Nucleus.

Post-translational modifications. Ubiquitinated by the CTLH E3 ubiquitin-protein ligase complex, leading to subsequent proteasomal degradation.

Isoforms (3)

UniProt ID	Names	Canonical?
O60381-1	1	yes
O60381-2	2
O60381-3	3

RefSeq proteins (2): NP_001231191, NP_036389* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003652	Ataxin_AXH_dom	Domain
IPR009071	HMG_box_dom	Domain
IPR036096	Ataxin_AXH_dom_sf	Homologous_superfamily
IPR036910	HMG_box_dom_sf	Homologous_superfamily
IPR039655	HBP1	Family

Pfam: PF00505, PF08517

UniProt features (24 total): helix 7, strand 6, turn 2, splice variant 2, sequence conflict 2, chain 1, domain 1, DNA-binding region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
3QVE	X-RAY DIFFRACTION	2.04
2E6O	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60381-F1	62.15	0.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 336 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, FREAC2_01, TGCACTT_MIR519C_MIR519B_MIR519A, ENK_UV_RESPONSE_KERATINOCYTE_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, TACAATC_MIR508, FOXO1_01, GGGTGGRR_PAX4_03, LEE_LIVER_CANCER_CIPROFIBRATE_DN, MARTINEZ_RB1_TARGETS_UP, NF1_Q6_01, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_REGULATION_OF_CELL_CYCLE, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, HP1SITEFACTOR_Q6

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), Wnt signaling pathway (GO:0016055), regulation of cell cycle (GO:0051726), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), RNA binding (GO:0003723), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
nucleic acid binding	2
cellular anatomical structure	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cell surface receptor signaling pathway	1
cell cycle	1
regulation of cellular process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
nuclear ribonucleoprotein granule	1

Protein interactions and networks

STRING

652 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HBP1	C1orf105	O95561	512
HBP1	ZNF24	P17028	446
HBP1	DUS4L	O95620	416
HBP1	RECK	O95980	413
HBP1	MTIF2	P46199	409
HBP1	NAA50	Q9GZZ1	403
HBP1	GPR22	Q99680	402
HBP1	COG5	Q9UP83	400
HBP1	ZBTB7A	O95365	395
HBP1	YAP1	P46937	381
HBP1	BMF	Q96LC9	378
HBP1	RNF11	Q9Y3C5	377
HBP1	DDIT4	Q9NX09	375
HBP1	ARID2	Q68CP9	365
HBP1	CCNG1	P51959	360

IntAct

22 interactions, top by confidence:

A	B	Type	Score
GID8	HTRA2	psi-mi:“MI:0914”(association)	0.610
HBP1	RB1	psi-mi:“MI:0915”(physical association)	0.400
RB1	HBP1	psi-mi:“MI:0915”(physical association)	0.400
CCL24	HBP1	psi-mi:“MI:0915”(physical association)	0.370
	HBP1	psi-mi:“MI:0915”(physical association)	0.370
ANKRD2	HBP1	psi-mi:“MI:0915”(physical association)	0.370
HBP1	TMEM37	psi-mi:“MI:0915”(physical association)	0.370
HBP1	SMAD1	psi-mi:“MI:0915”(physical association)	0.370
CASP8	HBP1	psi-mi:“MI:0915”(physical association)	0.370
ESR1	HBP1	psi-mi:“MI:0915”(physical association)	0.370
HBP1	RB1CC1	psi-mi:“MI:0915”(physical association)	0.370
ARMC8	VWA8	psi-mi:“MI:0914”(association)	0.350
GID8	PGRMC1	psi-mi:“MI:0914”(association)	0.350
RMND5A	HTRA2	psi-mi:“MI:0914”(association)	0.350
GID8	VWA8	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
ZNF212	HBP1	psi-mi:“MI:0915”(physical association)	0.000
HBP1	CD2AP	psi-mi:“MI:0915”(physical association)	0.000
EWSR1	HBP1	psi-mi:“MI:0915”(physical association)	0.000
HBP1	KIFBP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (144): HBP1 (Affinity Capture-MS), HBP1 (Affinity Capture-MS), HBP1 (Affinity Capture-Western), HBP1 (Two-hybrid), HBP1 (Two-hybrid), HBP1 (Two-hybrid), RB1 (Two-hybrid), RBL2 (Two-hybrid), HBP1 (Affinity Capture-MS), HBP1 (Affinity Capture-MS), HBP1 (Affinity Capture-MS), SAP130 (Affinity Capture-MS), ZCCHC3 (Affinity Capture-MS), RPL35A (Affinity Capture-MS), RSL1D1 (Affinity Capture-MS)

ESM2 similar proteins: A3FEM2, A8WFJ9, F1R8Z9, G5EC89, G5EFY5, L8E946, O60381, P10157, P11308, P19102, P22816, P26323, P41157, P41935, P51023, P53544, P81270, Q01414, Q01543, Q18579, Q1LVQ7, Q21263, Q22355, Q25132, Q28D67, Q28HT3, Q29RS8, Q5NDM2, Q63ZH2, Q6P2Z3, Q6P8A3, Q7ZYQ0, Q8AXW8, Q8GWP0, Q8ITI5, Q8JIT5, Q90837, Q90VZ9, Q90WN4, Q91712

Diamond homologs: A0A0G2JTZ2, A4IIJ8, A4QNG3, A5A763, B0ZTE2, B1H349, B3DLD3, B3DM43, B7ZR65, F1LYL9, F1M8W4, O18896, O42569, O55170, O60248, O60381, O94993, O95416, P35710, P35711, P35712, P35713, P40645, P40647, P40649, P43267, P43680, P48430, P48431, P48432, P48434, P48436, P54231, P56693, P57073, P57074, P61259, P61753, P61754, Q04886

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
MAPK11	up-regulates	HBP1	phosphorylation
MAPK14	up-regulates	HBP1	phosphorylation
HBP1	“down-regulates quantity by repression”	NCF1	“transcriptional regulation”
PIM1	“up-regulates activity”	HBP1	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1929 predictions. Top by Δscore:

Variant	Effect	Δscore
7:107179871:A:AG	acceptor_gain	1.0000
7:107179872:T:G	acceptor_gain	1.0000
7:107179876:A:AG	acceptor_gain	1.0000
7:107179877:A:G	acceptor_gain	1.0000
7:107179878:G:GG	acceptor_gain	1.0000
7:107179878:GTCA:G	acceptor_gain	1.0000
7:107180058:GCTTG:G	donor_gain	1.0000
7:107180059:CTTG:C	donor_gain	1.0000
7:107180060:TTGG:T	donor_loss	1.0000
7:107180061:TG:T	donor_gain	1.0000
7:107180061:TGG:T	donor_loss	1.0000
7:107180062:GG:G	donor_gain	1.0000
7:107180062:GGT:G	donor_loss	1.0000
7:107180063:G:GG	donor_gain	1.0000
7:107180063:G:T	donor_loss	1.0000
7:107182371:A:AG	acceptor_gain	1.0000
7:107182372:G:GA	acceptor_gain	1.0000
7:107182598:ATAG:A	donor_gain	1.0000
7:107182598:ATAGG:A	donor_loss	1.0000
7:107182600:AGGTA:A	donor_loss	1.0000
7:107182601:GGTA:G	donor_loss	1.0000
7:107182602:G:GG	donor_gain	1.0000
7:107182603:T:A	donor_loss	1.0000
7:107185796:TTTAG:T	acceptor_loss	1.0000
7:107185798:TA:T	acceptor_loss	1.0000
7:107185799:A:AG	acceptor_gain	1.0000
7:107185799:AG:A	acceptor_loss	1.0000
7:107185800:G:GA	acceptor_gain	1.0000
7:107185800:GAT:G	acceptor_gain	1.0000
7:107185800:GATC:G	acceptor_gain	1.0000

AlphaMissense

3399 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:107190175:T:A	W309R	1.000
7:107190175:T:C	W309R	1.000
7:107195875:T:C	L370S	1.000
7:107196072:A:G	R436G	1.000
7:107196073:G:C	R436T	1.000
7:107196074:A:C	R436S	1.000
7:107196074:A:T	R436S	1.000
7:107196075:C:A	P437T	1.000
7:107196075:C:T	P437S	1.000
7:107196076:C:A	P437Q	1.000
7:107196076:C:G	P437R	1.000
7:107196076:C:T	P437L	1.000
7:107196079:T:C	M438T	1.000
7:107196080:G:A	M438I	1.000
7:107196080:G:C	M438I	1.000
7:107196080:G:T	M438I	1.000
7:107196081:A:C	N439H	1.000
7:107196081:A:G	N439D	1.000
7:107196082:A:T	N439I	1.000
7:107196083:T:A	N439K	1.000
7:107196083:T:G	N439K	1.000
7:107196085:C:A	A440D	1.000
7:107196085:C:T	A440V	1.000
7:107196087:T:A	F441I	1.000
7:107196087:T:C	F441L	1.000
7:107196087:T:G	F441V	1.000
7:107196088:T:C	F441S	1.000
7:107196088:T:G	F441C	1.000
7:107196089:C:A	F441L	1.000
7:107196089:C:G	F441L	1.000

dbSNP variants (sampled 300 via entrez): RS1000030282 (7:107188430 G>T), RS1000038820 (7:107201574 AATAAT>A,AATAATATAAT), RS1000069837 (7:107183464 G>A), RS1000121449 (7:107183851 C>T), RS1000209160 (7:107168764 C>A,T), RS1000218503 (7:107168019 A>C,T), RS1000416340 (7:107170981 GTA>G,GTATA), RS1000498973 (7:107182246 A>G), RS1000625253 (7:107179252 C>T), RS1000881889 (7:107170818 C>T), RS1000945259 (7:107192663 T>C,G), RS1000966096 (7:107178923 A>G), RS1001041374 (7:107193727 C>T), RS1001060422 (7:107186945 A>G), RS1001156680 (7:107167769 C>T)

Disease associations

OMIM: gene MIM:616714 | disease phenotypes: MIM:613612

GenCC curated gene-disease

Mondo (1): COG5-congenital disorder of glycosylation (MONDO:0013325)

Orphanet (1): COG5-CDG (Orphanet:263487)

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST009391_1162	Metabolite levels	3.000000e-06
GCST009391_159	Metabolite levels	2.000000e-06
GCST009391_1665	Metabolite levels	1.000000e-06
GCST009391_1950	Metabolite levels	3.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0010460	anthranilic acid measurement
EFO:0010487	glutamate measurement
EFO:0010470	carnosine measurement
EFO:0010462	aspartate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	5
bisphenol A	increases expression, affects cotreatment, increases methylation, decreases methylation	3
Estradiol	decreases expression, increases expression	3
Valproic Acid	decreases expression, increases expression, affects expression	3
Cyclosporine	increases expression	3
cobaltous chloride	increases expression	2
Ethyl Methanesulfonate	decreases expression, increases expression	2
Methyl Methanesulfonate	decreases expression, increases expression	2
Niclosamide	decreases reaction, increases expression, decreases expression	2
Sirolimus	decreases reaction, affects cotreatment, affects expression, decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	increases expression	1
afuresertib	increases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
uranyl acetate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
geraniol	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
pyrvinium	decreases expression, decreases reaction	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
didecyldimethylammonium	increases expression	1
cupric oxide	increases expression	1
hydroquinone	affects binding, increases reaction	1
di-n-butylphosphoric acid	affects expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_HA16	MCF-7 eGFP-HBP1	Cancer cell line	Female

Clinical trials (associated diseases)

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