GPBP1L1

Summary

GPBP1L1 (GC-rich promoter binding protein 1 like 1, HGNC:28843) is a protein-coding gene on chromosome 1p34.1, encoding Vasculin-like protein 1 (Q9HC44). Possible transcription factor.

Predicted to enable DNA binding activity and RNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be active in nucleus.

Source: NCBI Gene 60313 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_021639

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28843
Approved symbol	GPBP1L1
Name	GC-rich promoter binding protein 1 like 1
Location	1p34.1
Locus type	gene with protein product
Status	Approved
Aliases	SP192
Ensembl gene	ENSG00000159592
Ensembl biotype	protein_coding
Entrez	60313

Gene structure

Transcript identifiers

Ensembl transcripts: 54 — 42 protein_coding, 12 protein_coding_CDS_not_defined

ENST00000290795, ENST00000355105, ENST00000460859, ENST00000467032, ENST00000468724, ENST00000479235, ENST00000480083, ENST00000480941, ENST00000487436, ENST00000488278, ENST00000493083, ENST00000495616, ENST00000496278, ENST00000498128, ENST00000871064, ENST00000871065, ENST00000871066, ENST00000871067, ENST00000871068, ENST00000871069, ENST00000871070, ENST00000871071, ENST00000871072, ENST00000871073, ENST00000871074, ENST00000871075, ENST00000871076, ENST00000871077, ENST00000871078, ENST00000871079, ENST00000871080, ENST00000871081, ENST00000871082, ENST00000871083, ENST00000871084, ENST00000871085, ENST00000871086, ENST00000871087, ENST00000871088, ENST00000871089, ENST00000917050, ENST00000917051, ENST00000917052, ENST00000917053, ENST00000917054, ENST00000917055, ENST00000917056, ENST00000917057, ENST00000955086, ENST00000955087, ENST00000955088, ENST00000955089, ENST00000955090, ENST00000955091

RefSeq mRNA: 1 — MANE Select: NM_021639 NM_021639

CCDS: CCDS528

Canonical transcript exons

ENST00000355105 — 13 exons

Exon	Start	End
ENSE00001408745	45660184	45661225
ENSE00001641952	45685576	45685620
ENSE00001736304	45686412	45686533
ENSE00003504674	45633489	45633647
ENSE00003513737	45627304	45628408
ENSE00003603987	45654543	45654829
ENSE00003612517	45642427	45642499
ENSE00003627881	45630482	45630606
ENSE00003646465	45629576	45629678
ENSE00003888737	45634096	45634236
ENSE00003888808	45659028	45659142
ENSE00003890209	45655190	45655319
ENSE00003891163	45640210	45640403

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.6270 / max 620.4743, expressed in 1820 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12150	29.1136	1815
12151	14.0582	1787
12153	1.7526	888
12154	1.0550	564
12149	0.6171	325
12152	0.6101	312
12148	0.4204	204

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	98.47	gold quality
lower esophagus mucosa	UBERON:0035834	97.85	gold quality
rectum	UBERON:0001052	97.61	gold quality
right testis	UBERON:0004534	97.28	gold quality
skin of leg	UBERON:0001511	97.03	gold quality
left testis	UBERON:0004533	97.02	gold quality
skin of abdomen	UBERON:0001416	97.01	gold quality
mucosa of transverse colon	UBERON:0004991	96.88	gold quality
sural nerve	UBERON:0015488	96.86	gold quality
transverse colon	UBERON:0001157	96.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.67	gold quality
testis	UBERON:0000473	96.64	gold quality
buccal mucosa cell	CL:0002336	96.63	gold quality
right lobe of thyroid gland	UBERON:0001119	96.63	gold quality
ectocervix	UBERON:0012249	96.63	gold quality
body of pancreas	UBERON:0001150	96.60	gold quality
minor salivary gland	UBERON:0001830	96.52	gold quality
vagina	UBERON:0000996	96.47	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.45	gold quality
tendon of biceps brachii	UBERON:0008188	96.43	gold quality
left lobe of thyroid gland	UBERON:0001120	96.42	gold quality
thyroid gland	UBERON:0002046	96.41	gold quality
right lobe of liver	UBERON:0001114	96.37	gold quality
esophagus mucosa	UBERON:0002469	96.32	gold quality
ileal mucosa	UBERON:0000331	96.31	gold quality
right lung	UBERON:0002167	96.31	gold quality
small intestine	UBERON:0002108	96.20	gold quality
tendon	UBERON:0000043	96.19	gold quality
monocyte	CL:0000576	96.17	gold quality
intestine	UBERON:0000160	96.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting GPBP1L1, 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-6873-3P	100.00	71.42	2626
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-3686	99.90	70.53	2432

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpbp1l1	ENSDARG00000075569
mus_musculus	Gpbp1l1	ENSMUSG00000034042
rattus_norvegicus	Gpbp1l2	ENSRNOG00000016336
rattus_norvegicus	LOC100361636	ENSRNOG00000033346
rattus_norvegicus	Gpbp1l1	ENSRNOG00000037595
rattus_norvegicus	Gpbp1l2	ENSRNOG00000046675

Paralogs (1): GPBP1 (ENSG00000062194)

Protein

Protein identifiers

Vasculin-like protein 1 — Q9HC44 (reviewed: Q9HC44)

Alternative names: GC-rich promoter-binding protein 1-like 1

All UniProt accessions (1): Q9HC44

UniProt curated annotations — full annotation on UniProt →

Function. Possible transcription factor.

Subcellular location. Nucleus.

Similarity. Belongs to the vasculin family.

RefSeq proteins (1): NP_067652* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028128	Vasculin_fam	Family

Pfam: PF15337

UniProt features (22 total): compositionally biased region 7, modified residue 6, region of interest 4, sequence variant 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9HC44-F1	55.20	0.05

Functional residue map

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

Post-translational modifications (6): 49, 76, 202, 292, 301, 382

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 170 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, TAATAAT_MIR126, RACCACAR_AML_Q6, TGACCTY_ERR1_Q2, MEF2_02, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, IRF1_Q6, chr1p34, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, TGAGATT_MIR216, VDR_Q3, AML1_01, CTAWWWATA_RSRFC4_Q2, TGACCTTG_SF1_Q6, DR3_Q4

GO Biological Process (3): DNA-templated transcription (GO:0006351), regulation of DNA-templated transcription (GO:0006355), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (3): DNA binding (GO:0003677), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	2
nucleic acid binding	2
gene expression	1
RNA biosynthetic process	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

548 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPBP1L1	TMEM69	Q5SWH9	741
GPBP1L1	MAST2	Q6P0Q8	583
GPBP1L1	ZNF700	Q9H0M5	571
GPBP1L1	EIF3B	P55884	481
GPBP1L1	CCDC17	Q96LX7	456
GPBP1L1	GOLGA8J	A6NMD2	447
GPBP1L1	CCDC163	A0A0D9SF12	445
GPBP1L1	KCNRG	Q8N5I3	399
GPBP1L1	TADA2A	O75478	396
GPBP1L1	CIMAP1D	Q3SX64	394
GPBP1L1	NASP	P49321	393
GPBP1L1	AKR1A1	P14550	363
GPBP1L1	PTAR1	Q7Z6K3	353
GPBP1L1	RANBP10	Q6VN20	350
GPBP1L1	CHODL	Q9H9P2	349

IntAct

56 interactions, top by confidence:

A	B	Type	Score
DDX19B	MIF4GD	psi-mi:“MI:0914”(association)	0.870
QRSL1	GATB	psi-mi:“MI:0914”(association)	0.790
GPBP1L1	CNOT11	psi-mi:“MI:0915”(physical association)	0.740
EIF3E	GPBP1L1	psi-mi:“MI:0915”(physical association)	0.660
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
GPBP1L1	FOS	psi-mi:“MI:0915”(physical association)	0.560
GPBP1L1	UQCRC1	psi-mi:“MI:0915”(physical association)	0.560
PIP4K2A	AP3B1	psi-mi:“MI:0914”(association)	0.530
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
GPBP1L1	CNOT1	psi-mi:“MI:0914”(association)	0.530
SNRPF	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
DCAF7	CLASP2	psi-mi:“MI:0914”(association)	0.510
GPBP1L1	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
GPBP1L1	LRRK1	psi-mi:“MI:0407”(direct interaction)	0.440
LRRK2	GPBP1L1	psi-mi:“MI:0407”(direct interaction)	0.440
FADS2	GPBP1L1	psi-mi:“MI:0915”(physical association)	0.400
GPBP1L1	PLEKHF2	psi-mi:“MI:0915”(physical association)	0.370
EWSR1	GPBP1L1	psi-mi:“MI:0915”(physical association)	0.370
CNOT1	IBTK	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
NANOS2	CNOT1	psi-mi:“MI:0914”(association)	0.350
GPBP1L1	CNOT1	psi-mi:“MI:0914”(association)	0.350
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.350

BioGRID (134): GPBP1L1 (Affinity Capture-RNA), GPBP1L1 (Two-hybrid), PLEKHF2 (Two-hybrid), GPBP1L1 (Two-hybrid), GPBP1L1 (Affinity Capture-MS), GPBP1L1 (Affinity Capture-MS), QRSL1 (Affinity Capture-MS), TC2N (Affinity Capture-MS), PLCD3 (Affinity Capture-MS), KANSL2 (Affinity Capture-MS), GPBP1L1 (Affinity Capture-MS), GPBP1L1 (Affinity Capture-MS), GPBP1L1 (Affinity Capture-MS), CNOT11 (Affinity Capture-MS), AMPD2 (Affinity Capture-MS)

ESM2 similar proteins: A8PUI7, B3H4F1, B3M0Y8, B3P4I7, B4GMI7, B4HI06, B4JUG8, B4KBL1, B4M5L0, B4N8G6, B4PU44, B4QU20, E7F568, F4I5N6, F4IVV0, O75167, P0CJ62, P97825, Q09JY9, Q15398, Q3KQW7, Q3KR53, Q3T0T5, Q4KLP8, Q52KW0, Q5R9C3, Q69Z38, Q6A0A2, Q6AWX6, Q6AXU6, Q6DD19, Q6DFV3, Q6IRN6, Q6NZP2, Q6P3A1, Q71M21, Q71RC2, Q7XQ83, Q801E2, Q8BWW4

Diamond homologs: Q0P5K1, Q28FE5, Q3KR53, Q5R4E9, Q5R9C3, Q6DD19, Q6NXH3, Q6NZP2, Q86WP2, Q9HC44

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 62 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
Activation of BAD and translocation to mitochondria	5	92.8×	2e-07
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	5	81.9×	2e-07
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	5	81.9×	2e-07
Activation of BH3-only proteins	5	60.5×	1e-06
RHO GTPases activate PKNs	5	38.7×	6e-06
Intrinsic Pathway for Apoptosis	5	35.7×	8e-06
SARS-CoV-1-host interactions	6	25.7×	4e-06
Transcriptional and post-translational regulation of MITF-M expression and activity	5	21.8×	8e-05

GO biological processes:

GO term	Partners	Fold	FDR
intracellular protein localization	6	11.0×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2681 predictions. Top by Δscore:

Variant	Effect	Δscore
1:45628404:CTCAG:C	acceptor_gain	1.0000
1:45628406:CAG:C	acceptor_gain	1.0000
1:45628407:AG:A	acceptor_gain	1.0000
1:45628409:C:CC	acceptor_gain	1.0000
1:45628411:A:C	acceptor_gain	1.0000
1:45628415:T:TC	acceptor_gain	1.0000
1:45628419:C:CT	acceptor_gain	1.0000
1:45628420:A:AC	acceptor_gain	1.0000
1:45628420:A:C	acceptor_gain	1.0000
1:45628420:A:T	acceptor_gain	1.0000
1:45629571:CATA:C	donor_loss	1.0000
1:45629572:ATACC:A	donor_loss	1.0000
1:45629573:TACCT:T	donor_loss	1.0000
1:45629574:A:C	donor_loss	1.0000
1:45629575:C:CG	donor_loss	1.0000
1:45629674:ATAAC:A	acceptor_gain	1.0000
1:45629675:TAAC:T	acceptor_gain	1.0000
1:45629677:ACC:A	acceptor_loss	1.0000
1:45629679:C:CG	acceptor_loss	1.0000
1:45629680:T:C	acceptor_loss	1.0000
1:45629687:C:CT	acceptor_gain	1.0000
1:45629689:C:CT	acceptor_gain	1.0000
1:45629690:A:T	acceptor_gain	1.0000
1:45630478:TTA:T	donor_loss	1.0000
1:45630479:TACCT:T	donor_loss	1.0000
1:45630480:A:AC	donor_gain	1.0000
1:45630481:C:CA	donor_loss	1.0000
1:45630481:C:CC	donor_gain	1.0000
1:45630481:CCT:C	donor_gain	1.0000
1:45630602:TCCAA:T	acceptor_gain	1.0000

AlphaMissense

3134 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:45659060:A:G	W10R	1.000
1:45659060:A:T	W10R	1.000
1:45629657:C:A	W397C	0.999
1:45629657:C:G	W397C	0.999
1:45629659:A:G	W397R	0.999
1:45629659:A:T	W397R	0.999
1:45629673:A:G	L392S	0.999
1:45629676:A:G	L391S	0.999
1:45659056:A:G	L11P	0.999
1:45659058:C:A	W10C	0.999
1:45659058:C:G	W10C	0.999
1:45659070:A:C	F6L	0.999
1:45659070:A:T	F6L	0.999
1:45659072:A:G	F6L	0.999
1:45629658:C:G	W397S	0.998
1:45630492:C:G	A387P	0.998
1:45633556:A:G	L326P	0.998
1:45633559:A:G	F325S	0.998
1:45642430:A:G	W183R	0.998
1:45642430:A:T	W183R	0.998
1:45654543:A:C	F159L	0.998
1:45654543:A:T	F159L	0.998
1:45654545:A:G	F159L	0.998
1:45659059:C:G	W10S	0.998
1:45659065:G:T	P8H	0.998
1:45659071:A:C	F6C	0.998
1:45659071:A:G	F6S	0.998
1:45629604:A:G	L415P	0.997
1:45629668:C:G	A394P	0.997
1:45633556:A:T	L326Q	0.997

dbSNP variants (sampled 300 via entrez): RS1000115167 (1:45649748 C>T), RS1000154561 (1:45687547 G>C,T), RS1000197700 (1:45673624 G>A), RS1000288893 (1:45646015 C>T), RS1000301260 (1:45684715 G>C), RS1000362907 (1:45644708 T>C), RS1000375617 (1:45633992 A>G), RS1000425496 (1:45638531 C>G), RS1000442109 (1:45640623 A>C), RS1000454063 (1:45678495 G>A), RS1000509784 (1:45647244 C>T), RS1000516917 (1:45654217 CAT>C), RS1000522229 (1:45685573 C>A), RS1000606688 (1:45664932 C>A,T), RS1000666672 (1:45659984 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary amenorrhea (MONDO:1060208)

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST004571_30	Iron status biomarkers (total iron binding capacity)	8.000000e-07
GCST004572_19	Iron status biomarkers (transferrin saturation)	8.000000e-07
GCST005951_37	Body mass index	8.000000e-10
GCST010696_7	Cortical thickness (min-P)	3.000000e-08
GCST010697_28	Cortical surface area (min-P)	2.000000e-08
GCST010698_30	Subcortical volume (min-P)	3.000000e-08
GCST010699_45	Brain morphology (min-P)	3.000000e-08
GCST010700_23	Cortical thickness (MOSTest)	1.000000e-10
GCST010701_9	Cortical surface area (MOSTest)	2.000000e-08
GCST010702_139	Subcortical volume (MOSTest)	4.000000e-14
GCST010703_258	Brain morphology (MOSTest)	2.000000e-13

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0006334	total iron binding capacity
EFO:0004340	body mass index
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	3
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
methylmercuric chloride	decreases expression	1
glycidyl methacrylate	increases expression	1
beta-lapachone	decreases expression	1
cobaltous chloride	increases expression	1
manganese chloride	increases expression, increases abundance	1
K 7174	increases expression	1
eprenetapopt	affects expression, affects reaction	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Caffeine	decreases phosphorylation	1
Carbamazepine	affects expression	1
Demecolcine	increases expression	1
Doxorubicin	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression	1
Urethane	increases expression	1
Vincristine	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A2H5	SEES3-1V human GPBP1L1, clone1	Embryonic stem cell	Male
CVCL_A2H6	SEES3-1V human GPBP1L1, clone2	Embryonic stem cell	Male
CVCL_A2H7	SEES3-1V human GPBP1L1, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT07164248	Not specified	COMPLETED	Evaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice