GREP1

Summary

GREP1 (glycine rich extracellular protein 1, HGNC:27549) is a protein-coding gene on chromosome 16p13.3, encoding Glycine-rich extracellular protein 1 (A0A0J9YXV3).

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001396456

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27549
Approved symbol	GREP1
Name	glycine rich extracellular protein 1
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	G029442
Ensembl gene	ENSG00000262152
Ensembl biotype	protein_coding
OMIM	621298
Entrez	283875

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 retained_intron, 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000571152, ENST00000572266, ENST00000573315, ENST00000573465, ENST00000715180, ENST00000715181, ENST00000715182, ENST00000715183, ENST00000715184, ENST00000715185, ENST00000715186, ENST00000715187, ENST00000715188

RefSeq mRNA: 5 — MANE Select: NM_001396456 NM_001396456, NM_001396457, NM_001396458, NM_001396460, NM_001396461

Canonical transcript exons

ENST00000715180 — 29 exons

Exon	Start	End
ENSE00002676825	3001281	3001334
ENSE00002679382	2999902	2999943
ENSE00003775565	2997803	2997835
ENSE00003776244	2996496	2996531
ENSE00003777270	2995619	2995654
ENSE00003777525	2998494	2998523
ENSE00003777709	2992931	2992963
ENSE00003777878	2991048	2991101
ENSE00003778154	2994806	2994838
ENSE00003778939	2990552	2990587
ENSE00003779520	3000086	3000118
ENSE00003779664	3000714	3000827
ENSE00003779697	2995284	2995316
ENSE00003780756	2989523	2989552
ENSE00003781348	2996673	2996705
ENSE00003781619	2989974	2990006
ENSE00003781901	2995739	2995771
ENSE00003782011	2998356	2998388
ENSE00003782202	2990087	2990122
ENSE00003782510	2992805	2992834
ENSE00003782764	2988590	2988622
ENSE00003783424	2998848	2998979
ENSE00003783590	2994927	2994962
ENSE00003783707	2994698	2994727
ENSE00004026083	2988262	2988340
ENSE00004026101	2992403	2992438
ENSE00004026106	2991378	2991437
ENSE00004026109	3001561	3002011
ENSE00004026121	2997053	2997085

Expression profiles

Bgee: expression breadth ubiquitous, 107 present calls, max score 90.91.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0365 / max 14.9209, expressed in 20 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152350	0.0365	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	90.91	gold quality
nasal cavity epithelium	UBERON:0005384	87.92	gold quality
epithelial cell of pancreas	CL:0000083	86.59	gold quality
left ventricle myocardium	UBERON:0006566	84.85	gold quality
superficial temporal artery	UBERON:0001614	84.46	gold quality
cerebellar vermis	UBERON:0004720	83.86	gold quality
parotid gland	UBERON:0001831	83.45	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.73	gold quality
myocardium	UBERON:0002349	81.78	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	81.59	gold quality
vastus lateralis	UBERON:0001379	80.55	gold quality
upper arm skin	UBERON:0004263	79.97	gold quality
gingival epithelium	UBERON:0001949	78.12	gold quality
lateral globus pallidus	UBERON:0002476	77.24	silver quality
vena cava	UBERON:0004087	75.87	silver quality
endothelial cell	CL:0000115	75.70	gold quality
gingiva	UBERON:0001828	75.67	gold quality
substantia nigra pars compacta	UBERON:0001965	75.45	gold quality
pons	UBERON:0000988	75.28	silver quality
body of tongue	UBERON:0011876	74.96	gold quality
biceps brachii	UBERON:0001507	74.55	gold quality
secondary oocyte	CL:0000655	73.87	silver quality
heart right ventricle	UBERON:0002080	73.57	gold quality
tendon of biceps brachii	UBERON:0008188	73.41	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	73.05	gold quality
thymus	UBERON:0002370	72.59	gold quality
pericardium	UBERON:0002407	72.36	gold quality
cartilage tissue	UBERON:0002418	72.18	gold quality
saphenous vein	UBERON:0007318	72.11	gold quality
tongue	UBERON:0001723	72.00	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.28

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

• LINC00514 promoted CDC23 expression via restraining miR-204-3p activity, leading to papillary thyroid cancer progression. (PMID:30553447)
• Long noncoding RNA LINC00514 accelerates pancreatic cancer progression by acting as a ceRNA of miR-28-5p to upregulate Rap1b expression. (PMID:32771045)
• LINC00514 promotes gastric cancer cell growth and EMT progression via miR-204-3p/KRAS. (PMID:33888645)
• LINC00514 promotes lipogenesis and tumor progression in esophageal squamous cell carcinoma by sponging miR378a5p to enhance SPHK1 expression. (PMID:34533201)
• LINC00514 facilitates cell proliferation, migration, invasion, and epithelial-mesenchymal transition in non-small cell lung cancer by acting on the Wnt/beta-catenin signaling pathway. (PMID:35653786)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Grep1	ENSMUSG00000043747
rattus_norvegicus	Grep1	ENSRNOG00000065545

Protein

Protein identifiers

Glycine-rich extracellular protein 1 — A0A0J9YXV3 (reviewed: A0A0J9YXV3)

Alternative names: Long intergenic non-protein coding RNA 514

All UniProt accessions (3): A0A0J9YXV3, A0AAQ5BID0, A0AAQ5BID5

RefSeq proteins (5): NP_001383385, NP_001383386, NP_001383387, NP_001383389, NP_001383390 (=MANE)

Domains & families (InterPro)

UniProt features (7 total): region of interest 3, compositionally biased region 2, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A0J9YXV3-F1	42.28	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): FOSTER_KDM1A_TARGETS_UP, NFKBIA_TARGET_GENES, ZNF423_TARGET_GENES, DESCARTES_MAIN_FETAL_DUCTAL_CELLS, DESCARTES_FETAL_PANCREAS_DUCTAL_CELLS, NKX2_5_TARGET_GENES, GENES_CORRELATED_WITH_COL1A1_DELETION, GSE37416_CTRL_VS_0H_F_TULARENSIS_LVS_NEUTROPHIL_UP, ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP, GSE37533_UNTREATED_VS_PIOGLIZATONE_TREATED_CD4_TCELL_FOXP3_TRASDUCED_CD4_TCELL_UP, chr16p13, GSE40666_WT_VS_STAT4_KO_CD8_TCELL_UP, GSE45365_BCELL_VS_CD8_TCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

84 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GREP1	CDC23	Q9UJX2	400
GREP1	AGO2	Q9UKV8	364
GREP1	HCFC1R1	Q9NWW0	286
GREP1	FLYWCH2	Q96CP2	286
GREP1	KREMEN2	Q8NCW0	253
GREP1	ACACA	Q13085	252
GREP1	THOC6	Q86W42	251
GREP1	FLYWCH1	Q4VC44	250
GREP1	BICDL2	A1A5D9	250
GREP1	FASN	P49327	244
GREP1	SPHK1	Q9NYA1	241
GREP1	SYNGR2	O43760	212
GREP1	MMUT	P22033	190
GREP1	EIF6	P56537	185
GREP1	AFMID	Q63HM1	183

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0J9YXV3, A0A172M4N0, A2VE23, A5PL33, C7EMF5, E7EW31, F1NSM7, I3L273, O15027, O48582, O55189, O55196, O97939, P0C671, P0DV77, P14138, Q14D33, Q1XI13, Q28989, Q3B7M4, Q4R729, Q5R7U0, Q5SWP3, Q62840, Q63003, Q6E0U4, Q6H236, Q6NUN9, Q6UXA7, Q7Z2K8, Q86UU5, Q8BM15, Q8K4E0, Q8K4L6, Q8N1P7, Q8N3D4, Q96D09, Q96JG9, Q9BGL9, Q9D7G9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

4 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

4760 predictions. Top by Δscore:

Variant	Effect	Δscore
16:2991097:GTCAG:G	donor_gain	1.0000
16:2991099:CAG:C	donor_loss	1.0000
16:2991101:GGTGA:G	donor_loss	1.0000
16:2991102:G:GG	donor_gain	1.0000
16:2994802:CCA:C	acceptor_loss	1.0000
16:2994804:A:AG	acceptor_gain	1.0000
16:2994804:A:AT	acceptor_loss	1.0000
16:2994805:G:GG	acceptor_gain	1.0000
16:2994837:AGGTG:A	donor_loss	1.0000
16:2994838:GGTG:G	donor_loss	1.0000
16:2994839:GTG:G	donor_loss	1.0000
16:2994840:T:A	donor_loss	1.0000
16:2995734:TCCA:T	acceptor_loss	1.0000
16:2995735:CCAG:C	acceptor_loss	1.0000
16:2995736:CA:C	acceptor_loss	1.0000
16:2995737:A:AG	acceptor_gain	1.0000
16:2995737:A:AT	acceptor_loss	1.0000
16:2995738:G:A	acceptor_loss	1.0000
16:2995738:G:GG	acceptor_gain	1.0000
16:2995768:CCAGG:C	donor_loss	1.0000
16:2995769:CAGG:C	donor_loss	1.0000
16:2995770:AGGT:A	donor_loss	1.0000
16:2995771:GGTGA:G	donor_loss	1.0000
16:2995772:G:GA	donor_loss	1.0000
16:2995773:T:G	donor_loss	1.0000
16:2996494:A:AG	acceptor_gain	1.0000
16:2996495:G:GG	acceptor_gain	1.0000
16:2996703:CAG:C	donor_loss	1.0000
16:2996706:G:T	donor_loss	1.0000
16:2996975:G:GT	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000023128 (16:3001362 G>A), RS1000170143 (16:2992915 C>G), RS1000199858 (16:2993126 G>C), RS1000308437 (16:2987661 C>A,G,T), RS1000467758 (16:2987834 G>T), RS1000509413 (16:2993993 A>G), RS1000706040 (16:2987617 G>T), RS1001053010 (16:2988892 C>G,T), RS1001061607 (16:2989244 C>T), RS1001128520 (16:2997018 T>A,C), RS1001145304 (16:2998868 G>A,T), RS1001198747 (16:3001133 T>C), RS1001226114 (16:2998321 G>T), RS1001308225 (16:2995700 C>G,T), RS1001336906 (16:2992352 A>C,G)

Disease associations

OMIM: gene MIM:621298 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
bisphenol A	increases expression	1
fipronil	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
DEET	affects cotreatment, decreases expression	1
Polyribonucleotides	decreases reaction, increases activity, affects binding	1
Triclosan	decreases expression	1
Particulate Matter	increases expression, increases abundance	1

Clinical trials (associated diseases)

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