GLIPR1L2

Summary

GLIPR1L2 (GLIPR1 like 2, HGNC:28592) is a protein-coding gene on chromosome 12q21.2, encoding GLIPR1-like protein 2 (Q4G1C9).

This gene encodes a member of the cysteine-rich secretory protein, antigen 5, and pathogenesis-related 1 superfamily. Members of this family have roles in a variety of processes, including cancer and immune defense. This gene is located in a cluster with two related genes on chromosome 12. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 144321 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_001270396

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28592
Approved symbol	GLIPR1L2
Name	GLIPR1 like 2
Location	12q21.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC39497
Ensembl gene	ENSG00000180481
Ensembl biotype	protein_coding
OMIM	610394
Entrez	144321

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000320460, ENST00000378692, ENST00000547164, ENST00000550916, ENST00000906733

RefSeq mRNA: 2 — MANE Select: NM_001270396 NM_001270396, NM_152436

CCDS: CCDS58258, CCDS9010

Canonical transcript exons

ENST00000550916 — 6 exons

Exon	Start	End
ENSE00001241280	75413598	75413701
ENSE00002356768	75391089	75391350
ENSE00002372073	75430824	75432688
ENSE00003477980	75422904	75422989
ENSE00003518556	75430715	75430741
ENSE00003664729	75410434	75410679

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 87.72.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4061 / max 139.3853, expressed in 461 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126900	1.4061	461

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	87.72	gold quality
testis	UBERON:0000473	87.68	gold quality
right testis	UBERON:0004534	86.54	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.82	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.74	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	77.55	gold quality
substantia nigra	UBERON:0002038	74.59	gold quality
islet of Langerhans	UBERON:0000006	73.11	gold quality
amygdala	UBERON:0001876	72.77	gold quality
temporal lobe	UBERON:0001871	72.57	gold quality
putamen	UBERON:0001874	72.28	gold quality
nucleus accumbens	UBERON:0001882	71.92	gold quality
Ammon’s horn	UBERON:0001954	71.50	gold quality
sural nerve	UBERON:0015488	71.42	gold quality
hypothalamus	UBERON:0001898	71.17	gold quality
caudate nucleus	UBERON:0001873	70.95	gold quality
skeletal muscle tissue	UBERON:0001134	68.85	gold quality
ventricular zone	UBERON:0003053	68.70	gold quality
left ovary	UBERON:0002119	68.61	gold quality
ovary	UBERON:0000992	68.42	gold quality
brain	UBERON:0000955	67.92	gold quality
cortical plate	UBERON:0005343	67.80	gold quality
muscle tissue	UBERON:0002385	67.60	gold quality
prefrontal cortex	UBERON:0000451	67.40	gold quality
cerebral cortex	UBERON:0000956	67.40	gold quality
primary visual cortex	UBERON:0002436	67.33	gold quality
anterior cingulate cortex	UBERON:0009835	66.91	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	66.78	gold quality
endocervix	UBERON:0000458	66.48	gold quality
frontal cortex	UBERON:0001870	66.40	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-CURD-89	no	275.43
E-ANND-3	no	4.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting GLIPR1L2, 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-5196-5P	100.00	67.98	2761
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-1179	99.71	68.70	1040
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-7156-5P	99.64	68.81	1369
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-548G-3P	99.48	68.67	2159

Cross-species orthologs

54 orthologs

Organism	Symbol	Gene ID
danio_rerio	glipr1b	ENSDARG00000030078
danio_rerio	glipr2	ENSDARG00000041724
danio_rerio	glipr1a	ENSDARG00000045224
danio_rerio		ENSDARG00000103034
danio_rerio	im:7150988	ENSDARG00000109310
mus_musculus	Glipr1l2	ENSMUSG00000020214
rattus_norvegicus	Glipr1l2	ENSRNOG00000049053
drosophila_melanogaster	Ag5r	FBGN0015010
drosophila_melanogaster	Ag5r2	FBGN0020508
drosophila_melanogaster	CG9400	FBGN0030562
drosophila_melanogaster	CG4270	FBGN0031407
drosophila_melanogaster	CG16995	FBGN0031412
drosophila_melanogaster	CG10651	FBGN0032853
drosophila_melanogaster	CG9822	FBGN0034623
drosophila_melanogaster	CG17974	FBGN0034624
drosophila_melanogaster	CG3640	FBGN0035042
drosophila_melanogaster	CG8072	FBGN0036070
drosophila_melanogaster	CG6628	FBGN0036072
drosophila_melanogaster	scpr-C	FBGN0037879
drosophila_melanogaster	scpr-B	FBGN0037888
drosophila_melanogaster	scpr-A	FBGN0037889
drosophila_melanogaster	CG8483	FBGN0038126
drosophila_melanogaster	CG30486	FBGN0050486
drosophila_melanogaster	antr	FBGN0050488
drosophila_melanogaster	CG31286	FBGN0051286
drosophila_melanogaster	CG32313	FBGN0052313
drosophila_melanogaster	CG32679	FBGN0052679
drosophila_melanogaster	CG34002	FBGN0054002
drosophila_melanogaster	CG34049	FBGN0054049
drosophila_melanogaster	CG17575	FBGN0250842
drosophila_melanogaster	CG42564	FBGN0260766
drosophila_melanogaster	CG42780	FBGN0261848
drosophila_melanogaster	CG43775	FBGN0264297
drosophila_melanogaster	CG43776	FBGN0264298
drosophila_melanogaster	CG43777	FBGN0264299
caenorhabditis_elegans		WBGENE00004742
caenorhabditis_elegans		WBGENE00007397
caenorhabditis_elegans		WBGENE00008027
caenorhabditis_elegans		WBGENE00008028
caenorhabditis_elegans		WBGENE00008029
caenorhabditis_elegans		WBGENE00008030
caenorhabditis_elegans		WBGENE00008625
caenorhabditis_elegans		WBGENE00009891
caenorhabditis_elegans		WBGENE00009895
caenorhabditis_elegans		WBGENE00009896
caenorhabditis_elegans		WBGENE00012816
caenorhabditis_elegans		WBGENE00013971
caenorhabditis_elegans		WBGENE00013972
caenorhabditis_elegans		WBGENE00015246
caenorhabditis_elegans		WBGENE00017055
caenorhabditis_elegans		WBGENE00017183
caenorhabditis_elegans		WBGENE00019178
caenorhabditis_elegans		WBGENE00019179
caenorhabditis_elegans		WBGENE00021780

Paralogs (13): CRISP3 (ENSG00000096006), R3HDML (ENSG00000101074), CRISPLD2 (ENSG00000103196), CRISPLD1 (ENSG00000121005), GLIPR2 (ENSG00000122694), CRISP2 (ENSG00000124490), CRISP1 (ENSG00000124812), PI15 (ENSG00000137558), GLIPR1 (ENSG00000139278), CLEC18B (ENSG00000140839), CLEC18A (ENSG00000157322), CLEC18C (ENSG00000157335), GLIPR1L1 (ENSG00000173401)

Protein

Protein identifiers

GLIPR1-like protein 2 — Q4G1C9 (reviewed: Q4G1C9)

All UniProt accessions (1): Q4G1C9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Highly expressed in testis. Detected in prostate, kidney, bladder, lung and bone marrow.

Induction. Up-regulated by doxycycline.

Similarity. Belongs to the CRISP family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q4G1C9-1	1, delta	yes
Q4G1C9-2	2, alpha
Q4G1C9-3	3
Q4G1C9-4	4, epsilon
Q4G1C9-5	5, gamma
Q4G1C9-6	6, beta

RefSeq proteins (2): NP_001257325, NP_689649 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001283	CRISP-related	Family
IPR014044	CAP_dom	Domain
IPR034121	SCP_GLIPR-1-like	Domain
IPR035940	CAP_sf	Homologous_superfamily

Pfam: PF00188

UniProt features (15 total): splice variant 8, compositionally biased region 3, chain 1, transmembrane region 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q4G1C9-F1	85.40	0.59

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): MARTINEZ_RB1_TARGETS_DN, chr12q21, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, E2F2_TARGET_GENES, EMX1_TARGET_GENES, HAND1_TARGET_GENES, HOXB4_TARGET_GENES, HOXD1_TARGET_GENES, LHX9_TARGET_GENES, MAFG_TARGET_GENES, RYBP_TARGET_GENES, TAFAZZIN_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF660_TARGET_GENES, ZNF664_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLIPR1L2	SPATA17	Q96L03	499
GLIPR1L2	DHRS13	Q6UX07	466
GLIPR1L2	TP53	P04637	463
GLIPR1L2	ATF7IP2	Q5U623	454
GLIPR1L2	FRY	Q5TBA9	453
GLIPR1L2	SUPT16H	Q9Y5B9	433
GLIPR1L2	SCN3A	Q9NY46	424
GLIPR1L2	PTK7	Q13308	415
GLIPR1L2	CACNA1G	O43497	409
GLIPR1L2	ARID1B	Q8NFD5	401
GLIPR1L2	ZNF98	A6NK75	392
GLIPR1L2	N4BP2L1	Q5TBK1	388
GLIPR1L2	TMEM14B	Q9NUH8	366
GLIPR1L2	TRIP12	Q14669	361
GLIPR1L2	DEXI	O95424	360

IntAct

5 interactions, top by confidence:

A	B	Type	Score
GLIPR1L2	PPP1CA	psi-mi:“MI:0915”(physical association)	0.370
GLIPR1L2	ZZEF1	psi-mi:“MI:0914”(association)	0.350
GLIPR1L2	PROS1	psi-mi:“MI:0914”(association)	0.350
GLIPR1L2	SEC24B	psi-mi:“MI:0914”(association)	0.350

BioGRID (33): ARMC8 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), MAEA (Affinity Capture-MS), MKLN1 (Affinity Capture-MS), RMND5A (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), RANBP9 (Affinity Capture-MS), GID4 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS), RANBP10 (Affinity Capture-MS), GID4 (Affinity Capture-MS), MKLN1 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), MAEA (Affinity Capture-MS), SNX11 (Affinity Capture-MS)

ESM2 similar proteins: A6QLZ7, D5K8A9, F8VQ03, H2QAR5, O77681, O95727, P0DV84, P14151, P30836, P35070, P48060, P51170, P97793, Q05928, Q0II64, Q149L7, Q28GB8, Q32LB5, Q4G1C9, Q4V9Y5, Q568T5, Q5XIG2, Q6PEW0, Q6UWM5, Q6UXB8, Q7M756, Q7T2X6, Q8BZQ2, Q8C0L0, Q8C351, Q8CGD2, Q8IUX8, Q91620, Q95237, Q98936, Q98ST5, Q9BXP8, Q9CQ35, Q9CWG1, Q9DA48

Diamond homologs: A2A5I3, A5D8T8, A6MFK9, A6QLZ7, A8S6B6, B0VXV6, B2MVK7, B7FDI0, B7FDI1, F8J2D4, F8S0Y4, G3CJR9, O19010, O43692, P07053, P08299, P09042, P0CB15, P0DMB9, P0DMT4, P0DPU0, P0DPU1, P0DPV2, P10737, P16562, P35760, P35780, P35781, P35782, P35783, P35784, P35785, P35786, P35787, P48060, P54108, P60623, P79845, P81657, P84805

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

872 predictions. Top by Δscore:

Variant	Effect	Δscore
12:75413597:GCTT:G	acceptor_gain	1.0000
12:75415706:T:A	acceptor_gain	1.0000
12:75422895:T:TA	acceptor_gain	1.0000
12:75422899:TGTA:T	acceptor_loss	1.0000
12:75422900:GTA:G	acceptor_loss	1.0000
12:75422902:A:AG	acceptor_gain	1.0000
12:75422902:AGAG:A	acceptor_gain	1.0000
12:75422903:G:GT	acceptor_gain	1.0000
12:75422903:GA:G	acceptor_gain	1.0000
12:75422903:GAGG:G	acceptor_gain	1.0000
12:75422903:GAGGA:G	acceptor_gain	1.0000
12:75391282:GA:G	donor_gain	0.9900
12:75391284:G:GG	donor_gain	0.9900
12:75391331:GGTC:G	donor_gain	0.9900
12:75391360:G:GT	donor_gain	0.9900
12:75403015:A:AG	acceptor_gain	0.9900
12:75403016:G:GG	acceptor_gain	0.9900
12:75403016:GTT:G	acceptor_gain	0.9900
12:75403016:GTTAT:G	acceptor_gain	0.9900
12:75409250:G:GT	donor_gain	0.9900
12:75410540:AT:A	acceptor_gain	0.9900
12:75410541:T:TA	acceptor_gain	0.9900
12:75413596:A:AG	acceptor_gain	0.9900
12:75413597:G:GG	acceptor_gain	0.9900
12:75413700:GG:G	donor_gain	0.9900
12:75413701:GG:G	donor_gain	0.9900
12:75415736:T:TA	acceptor_gain	0.9900
12:75422751:G:T	donor_gain	0.9900
12:75422774:G:GG	donor_gain	0.9900
12:75422899:T:TA	acceptor_gain	0.9900

AlphaMissense

2286 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:75410439:G:C	W80C	0.999
12:75410439:G:T	W80C	0.999
12:75410437:T:A	W80R	0.998
12:75410437:T:C	W80R	0.998
12:75410610:G:C	W137C	0.998
12:75410610:G:T	W137C	0.998
12:75413686:G:A	C190Y	0.998
12:75410441:A:T	D81V	0.997
12:75413625:G:T	G170C	0.997
12:75413628:T:A	C171S	0.997
12:75413629:G:C	C171S	0.997
12:75413685:T:A	C190S	0.997
12:75413686:G:C	C190S	0.997
12:75413687:C:G	C190W	0.997
12:75430849:G:C	W241C	0.997
12:75430849:G:T	W241C	0.997
12:75410456:G:C	R86P	0.996
12:75410581:T:C	F128L	0.996
12:75410583:T:A	F128L	0.996
12:75410583:T:G	F128L	0.996
12:75410608:T:A	W137R	0.996
12:75410608:T:C	W137R	0.996
12:75422986:T:A	C223S	0.996
12:75422987:G:C	C223S	0.996
12:75410462:C:A	A88D	0.995
12:75410482:T:A	C95S	0.995
12:75410483:G:C	C95S	0.995
12:75410582:T:G	F128C	0.995
12:75413626:G:A	G170D	0.995
12:75413628:T:C	C171R	0.995

dbSNP variants (sampled 300 via entrez): RS1000015122 (12:75397258 CT>C,CTT), RS1000042437 (12:75405769 T>A), RS1000070471 (12:75431957 A>C), RS1000122458 (12:75419390 A>G), RS1000233712 (12:75404511 A>G), RS1000411016 (12:75400526 A>G,T), RS1000492341 (12:75414435 A>G), RS1000603977 (12:75429420 A>G), RS1000646203 (12:75407106 C>T), RS1000706590 (12:75394280 A>G,T), RS1000731678 (12:75423905 T>C), RS1000774927 (12:75414171 T>C), RS1000777664 (12:75407662 G>A,T), RS1000844033 (12:75405805 A>G), RS1000949589 (12:75399542 C>T)

Disease associations

OMIM: gene MIM:610394 | 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
GCST003518_77	Daytime sleep phenotypes	8.000000e-06
GCST012490_431	Femur bone mineral density x serum urate levels interaction	2.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007828	daytime rest measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	affects cotreatment, increases expression	1
bisphenol A	affects cotreatment, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
pentanal	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Valproic Acid	decreases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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