GPALPP1

Summary

GPALPP1 (GPALPP motifs containing 1, HGNC:20298) is a protein-coding gene on chromosome 13q14.12, encoding GPALPP motifs-containing protein 1 (Q8IXQ4).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_018559

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20298
Approved symbol	GPALPP1
Name	GPALPP motifs containing 1
Location	13q14.12
Locus type	gene with protein product
Status	Approved
Aliases	bA245H20.2, AD029, LSR7
Ensembl gene	ENSG00000133114
Ensembl biotype	protein_coding
Entrez	55425

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000357537, ENST00000361121, ENST00000379151, ENST00000473119, ENST00000479068, ENST00000497558, ENST00000611650, ENST00000904226, ENST00000904227, ENST00000904228, ENST00000923873, ENST00000923874, ENST00000923875, ENST00000955038

RefSeq mRNA: 3 — MANE Select: NM_018559 NM_001316951, NM_001316952, NM_018559

CCDS: CCDS9394

Canonical transcript exons

ENST00000379151 — 8 exons

Exon	Start	End
ENSE00000907561	45015432	45015596
ENSE00000907562	45020330	45020428
ENSE00001253851	45004305	45004437
ENSE00001417511	44989538	44989742
ENSE00001534366	45027785	45030305
ENSE00003479690	45014952	45015083
ENSE00003658438	45008795	45008879
ENSE00003684155	45006202	45006303

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 93.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.6021 / max 292.7918, expressed in 1814 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134948	20.2112	1809
134949	3.3909	1507

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	93.24	gold quality
Brodmann (1909) area 23	UBERON:0013554	91.06	gold quality
cerebellar hemisphere	UBERON:0002245	89.32	gold quality
cerebellar cortex	UBERON:0002129	89.27	gold quality
calcaneal tendon	UBERON:0003701	89.21	gold quality
middle temporal gyrus	UBERON:0002771	89.10	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.56	gold quality
primary visual cortex	UBERON:0002436	88.32	gold quality
cerebellum	UBERON:0002037	87.96	gold quality
nucleus accumbens	UBERON:0001882	87.50	gold quality
anterior cingulate cortex	UBERON:0009835	87.39	gold quality
cingulate cortex	UBERON:0003027	87.24	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.09	gold quality
caudate nucleus	UBERON:0001873	86.79	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.61	gold quality
right frontal lobe	UBERON:0002810	86.43	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.84	gold quality
tendon	UBERON:0000043	85.77	gold quality
body of uterus	UBERON:0009853	85.76	gold quality
colonic epithelium	UBERON:0000397	85.75	gold quality
left ovary	UBERON:0002119	85.60	gold quality
occipital lobe	UBERON:0002021	85.58	gold quality
adrenal tissue	UBERON:0018303	85.52	gold quality
amygdala	UBERON:0001876	85.41	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.14	gold quality
telencephalon	UBERON:0001893	85.08	gold quality
right ovary	UBERON:0002118	85.07	gold quality
neocortex	UBERON:0001950	84.92	gold quality
adenohypophysis	UBERON:0002196	84.88	gold quality
cerebral cortex	UBERON:0000956	84.87	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-6911	no	119.94
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting GPALPP1, 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-3163	100.00	77.23	8605
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
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-651-3P	99.94	73.48	5177
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-154-5P	98.92	66.65	733
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-496	98.66	69.80	931
HSA-MIR-18B-3P	98.05	65.55	595
HSA-MIR-875-5P	96.74	66.48	579
HSA-MIR-6834-5P	96.25	64.88	823
HSA-MIR-3157-3P	95.86	67.08	454
HSA-MIR-4772-5P	95.60	68.04	617

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpalpp1	ENSDARG00000058287
drosophila_melanogaster	CG33332	FBGN0067629

Protein

Protein identifiers

GPALPP motifs-containing protein 1 — Q8IXQ4 (reviewed: Q8IXQ4)

Alternative names: Lipopolysaccharide-specific response protein 7

All UniProt accessions (3): A0A087WW86, A0A0A0MRI1, Q8IXQ4

UniProt curated annotations — full annotation on UniProt →

Isoforms (4)

UniProt ID	Names	Canonical?
Q8IXQ4-1	1	yes
Q8IXQ4-2	2
Q8IXQ4-3	3
Q8IXQ4-4	4

RefSeq proteins (3): NP_001303880, NP_001303881, NP_061029* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022226	DUF3752	Domain
IPR046331	GPAM1-like	Family

Pfam: PF12572

UniProt features (32 total): compositionally biased region 7, modified residue 6, sequence conflict 6, splice variant 4, short sequence motif 4, cross-link 2, initiator methionine 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IXQ4-F1	69.81	0.12

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 (8): 2, 28, 105, 138, 140, 141, 271, 308

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 99 (showing top): MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN, CREB_Q3, chr13q14, KIM_WT1_TARGETS_DN, MGGAAGTG_GABP_B, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, ZHAN_MULTIPLE_MYELOMA_MS_DN, CAMPS_COLON_CANCER_COPY_NUMBER_UP, HAMAI_APOPTOSIS_VIA_TRAIL_UP, DIDO1_TARGET_GENES, DLX4_TARGET_GENES, FOXG1_TARGET_GENES, SKIL_TARGET_GENES, TEAD2_TARGET_GENES, ZBTB12_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

672 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPALPP1	CCDC82	Q8N4S0	591
GPALPP1	WDR6	Q9NNW5	542
GPALPP1	LRRC2	Q9BYS8	537
GPALPP1	TBL2	Q9Y4P3	501
GPALPP1	TMCO1	Q9UM00	490
GPALPP1	PTDSS1	P48651	473
GPALPP1	XRRA1	Q6P2D8	454
GPALPP1	PRMT2IP	Q6ZRI6	434
GPALPP1	GTPBP8	Q8N3Z3	423
GPALPP1	MYG1	Q9HB07	406
GPALPP1	SPTLC1	O15269	402
GPALPP1	ZSCAN26	Q16670	377
GPALPP1	ADPRH	P54922	373
GPALPP1	E7EVR1	E7EVR1	365
GPALPP1	KRT27	Q7Z3Y8	349

IntAct

44 interactions, top by confidence:

A	B	Type	Score
PPIL1	SNW1	psi-mi:“MI:0914”(association)	0.930
CDK8	MED19	psi-mi:“MI:2364”(proximity)	0.850
CTBP2	ZNF217	psi-mi:“MI:0914”(association)	0.690
CAMKV	AP3B1	psi-mi:“MI:0914”(association)	0.640
PIP4K2A	AP3B1	psi-mi:“MI:0914”(association)	0.530
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530
ZNF816	LRP4	psi-mi:“MI:0914”(association)	0.530
ZNF311	CENPB	psi-mi:“MI:0914”(association)	0.530
ZNF786	NKTR	psi-mi:“MI:0914”(association)	0.530
ATXN3	GPALPP1	psi-mi:“MI:0915”(physical association)	0.400
THOC2		psi-mi:“MI:0914”(association)	0.350
Rhoa	CLK2	psi-mi:“MI:0914”(association)	0.350
Smad3		psi-mi:“MI:0914”(association)	0.350
Wdr48	DMWD	psi-mi:“MI:0914”(association)	0.350
Cetn2	SFI1	psi-mi:“MI:0914”(association)	0.350
Chmp6	NSF	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
GPALPP1	CDC37	psi-mi:“MI:0914”(association)	0.350
RNPS1	C1orf226	psi-mi:“MI:0914”(association)	0.350
PLCD3	AP3B1	psi-mi:“MI:0914”(association)	0.350
ARGLU1	CASC3	psi-mi:“MI:0914”(association)	0.350
NKAPD1	CASC3	psi-mi:“MI:0914”(association)	0.350
CLK2	CASC3	psi-mi:“MI:0914”(association)	0.350
PPIL3	SNX3	psi-mi:“MI:0914”(association)	0.350
ARL6IP4	EIF3J	psi-mi:“MI:0914”(association)	0.350
PPIA	SMARCA2	psi-mi:“MI:0914”(association)	0.350
ZNF816	TRIM37	psi-mi:“MI:0914”(association)	0.350
PIP4K2A	SAP18	psi-mi:“MI:0914”(association)	0.350
SIRT5	YEATS4	psi-mi:“MI:0914”(association)	0.350

BioGRID (66): GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Proximity Label-MS), GPALPP1 (Proximity Label-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS), GPALPP1 (Affinity Capture-MS)

ESM2 similar proteins: A6QPE1, B8B2G4, F4HVZ5, F4I700, F4JCU0, F4JP52, F4KIA8, O43031, O80386, O81242, Q0P4A6, Q10580, Q24K12, Q28C44, Q2TBE0, Q3UHX0, Q3ZBM6, Q4V893, Q5F3D1, Q5M9Q1, Q5R863, Q5R939, Q63ZM9, Q67VW6, Q67W65, Q69ZC8, Q6AWX6, Q6DJ13, Q6NZY4, Q6PUA2, Q76FK4, Q875B6, Q8BG79, Q8GXN9, Q8IXQ4, Q8LRK9, Q8RX78, Q8VY15, Q8VZ67, Q94C11

Diamond homologs: Q3ZBM6, Q4V893, Q5R863, Q69ZC8, Q8IXQ4, Q93591

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 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
Transport of Mature Transcript to Cytoplasm	5	43.3×	4e-06
RNA Polymerase II Transcription Termination	5	25.0×	6e-05
mRNA Splicing	9	22.5×	1e-08
Processing of Capped Intron-Containing Pre-mRNA	12	22.4×	1e-11
mRNA 3’-end processing	5	22.4×	9e-05
mRNA Splicing - Major Pathway	14	17.4×	6e-12
Transport of Mature mRNA derived from an Intron-Containing Transcript	5	17.3×	3e-04
Dengue Virus-Host Interactions	10	10.4×	2e-06

GO biological processes:

GO term	Partners	Fold	FDR
mRNA splicing, via spliceosome	12	21.6×	8e-11
RNA splicing	10	17.3×	4e-08
protein folding	7	14.2×	4e-05
mRNA processing	8	12.3×	3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1303 predictions. Top by Δscore:

Variant	Effect	Δscore
13:44989740:CTGGT:C	donor_loss	1.0000
13:44989741:TGG:T	donor_loss	1.0000
13:44989743:G:GG	donor_gain	1.0000
13:44989743:GTA:G	donor_loss	1.0000
13:44989744:T:G	donor_loss	1.0000
13:45004434:CAAG:C	donor_loss	1.0000
13:45004435:AAG:A	donor_loss	1.0000
13:45004436:AGGTC:A	donor_loss	1.0000
13:45004437:GGTC:G	donor_loss	1.0000
13:45004439:T:A	donor_loss	1.0000
13:45006197:TTCAG:T	acceptor_loss	1.0000
13:45006198:TCAG:T	acceptor_loss	1.0000
13:45006200:A:AG	acceptor_gain	1.0000
13:45006200:AG:A	acceptor_loss	1.0000
13:45006201:G:GG	acceptor_gain	1.0000
13:45006201:GA:G	acceptor_gain	1.0000
13:45006201:GAA:G	acceptor_gain	1.0000
13:45006287:G:GT	donor_gain	1.0000
13:45006301:AAGG:A	donor_loss	1.0000
13:45006302:AGGTG:A	donor_loss	1.0000
13:45006304:G:GC	donor_loss	1.0000
13:45006305:T:A	donor_loss	1.0000
13:45015080:TGAT:T	donor_gain	1.0000
13:45015081:GAT:G	donor_gain	1.0000
13:45015081:GATG:G	donor_gain	1.0000
13:45015082:AT:A	donor_gain	1.0000
13:45015083:TG:T	donor_loss	1.0000
13:45015084:G:GG	donor_gain	1.0000
13:45015084:GTAAG:G	donor_loss	1.0000
13:45015085:T:A	donor_loss	1.0000

AlphaMissense

2264 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:45015462:T:A	W191R	0.999
13:45015462:T:C	W191R	0.999
13:45015464:G:C	W191C	0.999
13:45015464:G:T	W191C	0.999
13:45015466:T:C	M192T	0.998
13:45015558:T:A	W223R	0.998
13:45015558:T:C	W223R	0.998
13:45015560:G:C	W223C	0.998
13:45015560:G:T	W223C	0.998
13:45027971:T:C	F331L	0.998
13:45027973:T:A	F331L	0.998
13:45027973:T:G	F331L	0.998
13:45015455:A:C	R188S	0.997
13:45015455:A:T	R188S	0.997
13:45015516:T:C	F209L	0.997
13:45015518:T:A	F209L	0.997
13:45015518:T:G	F209L	0.997
13:45027881:T:C	F301L	0.997
13:45027883:T:A	F301L	0.997
13:45027883:T:G	F301L	0.997
13:45027900:T:C	L307P	0.997
13:45027972:T:C	F331S	0.996
13:45015454:G:C	R188T	0.995
13:45015463:G:C	W191S	0.995
13:45015517:T:C	F209S	0.994
13:45027818:C:G	H280D	0.994
13:45027950:T:C	S324P	0.994
13:45015462:T:G	W191G	0.993
13:45027939:T:C	L320P	0.993
13:45015045:G:C	A168P	0.992

dbSNP variants (sampled 300 via entrez): RS1000050975 (13:45020678 A>C), RS1000129415 (13:44994088 C>T), RS1000133887 (13:44991239 G>C), RS1000151167 (13:45028459 A>G), RS1000172769 (13:45003515 T>A), RS1000192115 (13:44995511 C>A,G), RS1000422392 (13:44996194 A>G), RS1000634541 (13:44994372 C>T), RS1000663120 (13:45011281 G>A), RS1000671986 (13:45003034 A>G), RS1000733179 (13:44999817 A>G), RS1000759652 (13:45000844 A>G), RS1000802325 (13:44988675 G>C), RS1000884788 (13:45032370 A>G), RS1000908133 (13:44992238 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004611_193	High light scatter reticulocyte count	3.000000e-10
GCST004612_127	High light scatter reticulocyte percentage of red cells	8.000000e-11
GCST004628_55	Immature fraction of reticulocytes	6.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	7
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
FR900359	increases phosphorylation	1
TAK-243	decreases sumoylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases expression	1
butyraldehyde	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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