PLEKHJ1

Summary

PLEKHJ1 (pleckstrin homology domain containing J1, HGNC:18211) is a protein-coding gene on chromosome 19p13.3, encoding Pleckstrin homology domain-containing family J member 1 (Q9NW61).

Predicted to be involved in endosome organization; receptor recycling; and retrograde transport, endosome to Golgi. Predicted to be located in Golgi apparatus; cytoplasmic vesicle; and cytosol. Predicted to be active in early endosome; recycling endosome; and trans-Golgi network.

Source: NCBI Gene 55111 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_018049

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18211
Approved symbol	PLEKHJ1
Name	pleckstrin homology domain containing J1
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10297
Ensembl gene	ENSG00000104886
Ensembl biotype	protein_coding
OMIM	617834
Entrez	55111

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 14 protein_coding, 5 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000326631, ENST00000585423, ENST00000586497, ENST00000586608, ENST00000587394, ENST00000587962, ENST00000588356, ENST00000588450, ENST00000588545, ENST00000588633, ENST00000589097, ENST00000589791, ENST00000591099, ENST00000863429, ENST00000863430, ENST00000935575, ENST00000935576, ENST00000935577, ENST00000951302, ENST00000951303, ENST00000951304

RefSeq mRNA: 2 — MANE Select: NM_018049 NM_001300836, NM_018049

CCDS: CCDS12083, CCDS74251

Canonical transcript exons

ENST00000326631 — 6 exons

Exon	Start	End
ENSE00001288944	2236155	2236329
ENSE00002780885	2233153	2233905
ENSE00003504886	2235923	2235990
ENSE00003560129	2235762	2235828
ENSE00003610414	2234150	2234240
ENSE00003623163	2233998	2234061

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.3455 / max 168.8527, expressed in 1819 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178145	15.1496	1814
178144	11.9373	1783
178143	1.2066	720
178148	0.9456	438
178146	0.7762	492
178142	0.3029	133
178147	0.0273	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	98.74	gold quality
duodenum	UBERON:0002114	97.64	gold quality
transverse colon	UBERON:0001157	96.75	gold quality
left testis	UBERON:0004533	96.69	gold quality
right testis	UBERON:0004534	96.63	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.41	gold quality
body of pancreas	UBERON:0001150	96.36	gold quality
body of stomach	UBERON:0001161	96.20	gold quality
right lobe of thyroid gland	UBERON:0001119	96.09	gold quality
apex of heart	UBERON:0002098	96.07	gold quality
small intestine	UBERON:0002108	96.06	gold quality
adult mammalian kidney	UBERON:0000082	95.78	gold quality
left lobe of thyroid gland	UBERON:0001120	95.70	gold quality
metanephros cortex	UBERON:0010533	95.68	gold quality
ventricular zone	UBERON:0003053	95.60	gold quality
fundus of stomach	UBERON:0001160	95.51	gold quality
testis	UBERON:0000473	95.42	gold quality
heart left ventricle	UBERON:0002084	95.30	gold quality
lower esophagus mucosa	UBERON:0035834	95.07	gold quality
stomach	UBERON:0000945	95.00	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.00	gold quality
thyroid gland	UBERON:0002046	94.97	gold quality
gastrocnemius	UBERON:0001388	94.89	gold quality
intestine	UBERON:0000160	94.82	gold quality
colon	UBERON:0001155	94.75	gold quality
right adrenal gland	UBERON:0001233	94.72	gold quality
ganglionic eminence	UBERON:0004023	94.61	gold quality
granulocyte	CL:0000094	94.59	gold quality
right adrenal gland cortex	UBERON:0035827	94.53	gold quality
left adrenal gland	UBERON:0001234	94.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-6524	no	348.30
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting PLEKHJ1, 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-513A-5P	100.00	69.77	2465
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-593-5P	99.34	69.50	965

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	plekhj1	ENSDARG00000025593
mus_musculus	Plekhj1	ENSMUSG00000035278
rattus_norvegicus		ENSRNOG00000075264

Paralogs (2): PHETA2 (ENSG00000177096), PHETA1 (ENSG00000198324)

Protein

Protein identifiers

Pleckstrin homology domain-containing family J member 1 — Q9NW61 (reviewed: Q9NW61)

Alternative names: Guanine nucleotide-releasing protein x

All UniProt accessions (5): Q9NW61, K7EIW9, K7EIZ3, K7ERH2, K7ERW3

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in testis and liver.

RefSeq proteins (2): NP_001287765, NP_060519* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001849	PH_domain	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR045188	Boi1/Boi2-like	Family

Pfam: PF00169

UniProt features (2 total): chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NW61-F1	91.16	0.82

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): GOBP_ENDOSOME_ORGANIZATION, GOBP_VESICLE_ORGANIZATION, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_RECEPTOR_METABOLIC_PROCESS, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_RETROGRADE_TRANSPORT_ENDOSOME_TO_GOLGI, GOBP_CYTOSOLIC_TRANSPORT, chr19p13, GOCC_RECYCLING_ENDOSOME, GOCC_ORGANELLE_SUBCOMPARTMENT, WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP, LU_EZH2_TARGETS_UP, GOBP_RECEPTOR_RECYCLING

GO Biological Process (3): receptor recycling (GO:0001881), endosome organization (GO:0007032), retrograde transport, endosome to Golgi (GO:0042147)

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

GO Cellular Component (8): early endosome (GO:0005769), trans-Golgi network (GO:0005802), cytosol (GO:0005829), recycling endosome (GO:0055037), endosome (GO:0005768), Golgi apparatus (GO:0005794), clathrin-coated vesicle (GO:0030136), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	3
endosome	2
endomembrane system	2
endocytosis	1
receptor metabolic process	1
endomembrane system organization	1
vesicle organization	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
binding	1
Golgi apparatus subcompartment	1
cellular anatomical structure	1
cytoplasmic vesicle	1
intracellular membrane-bounded organelle	1
coated vesicle	1
intracellular vesicle	1

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PLEKHJ1	SF3A2	Q15428	488
PLEKHJ1	OR8K5	Q8NH50	478
PLEKHJ1	ZNF574	Q6ZN55	477
PLEKHJ1	OR5J2	Q8NH18	469
PLEKHJ1	ZMYND19	Q96E35	445
PLEKHJ1	PPP1R35	Q8TAP8	419
PLEKHJ1	GPATCH1	Q9BRR8	376
PLEKHJ1	ZNF460	Q14592	376
PLEKHJ1	ZNF101	Q8IZC7	371
PLEKHJ1	METTL23	Q86XA0	370
PLEKHJ1	PSMG3	Q9BT73	323
PLEKHJ1	RGL3	Q3MIN7	323
PLEKHJ1	ATP5MJ	P56378	321
PLEKHJ1	PTP4A3	O75365	320
PLEKHJ1	STX10	O60499	310

IntAct

37 interactions, top by confidence:

A	B	Type	Score
PHETA2	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.740
PLEKHJ1	PHETA1	psi-mi:“MI:0915”(physical association)	0.660
GPX7	GAK	psi-mi:“MI:0914”(association)	0.640
PIH1D2	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.560
PHETA1	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.560
LAGE3	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.560
NTAQ1	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.560
PHETA2	SEMG1	psi-mi:“MI:0914”(association)	0.530
PLEKHJ1	OCRL	psi-mi:“MI:0914”(association)	0.530
PLEKHJ1	DNMT3B	psi-mi:“MI:0915”(physical association)	0.370
PPBP	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
OCRL	ERC2	psi-mi:“MI:0914”(association)	0.350
OCRL	MYO1C	psi-mi:“MI:0914”(association)	0.350
PHETA2	NMT2	psi-mi:“MI:0914”(association)	0.350
OCRL	AP2A1	psi-mi:“MI:0914”(association)	0.350
PHETA1	INPP5B	psi-mi:“MI:0914”(association)	0.350
OCRL	LTF	psi-mi:“MI:0914”(association)	0.350
PLEKHJ1	AP3B1	psi-mi:“MI:0914”(association)	0.350
PHETA2	INPP5B	psi-mi:“MI:0914”(association)	0.350
PLEKHJ1	DENND4B	psi-mi:“MI:0914”(association)	0.350
RNPS1	WWP2	psi-mi:“MI:0914”(association)	0.350
PINX1	PLEKHJ1	psi-mi:“MI:0915”(physical association)	0.000
PLEKHJ1	KRT33B	psi-mi:“MI:0915”(physical association)	0.000
PLEKHJ1	PHETA1	psi-mi:“MI:0915”(physical association)	0.000
PLEKHJ1	LAGE3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (40): PLEKHJ1 (Affinity Capture-MS), PLEKHJ1 (Affinity Capture-MS), PLEKHJ1 (Affinity Capture-MS), PLEKHJ1 (Affinity Capture-MS), PLEKHJ1 (Affinity Capture-MS), PLEKHJ1 (Affinity Capture-MS), KRT33B (Affinity Capture-MS), PIH1D2 (Two-hybrid), WDYHV1 (Two-hybrid), FAM109B (Two-hybrid), LAGE3 (Two-hybrid), FAM109A (Two-hybrid), PLEKHJ1 (Affinity Capture-MS), PLEKHJ1 (Affinity Capture-MS), AP3B1 (Affinity Capture-MS)

ESM2 similar proteins: A6QLK6, O14508, O35717, O70277, O75382, O88582, O95057, P09851, P20936, P49138, P50904, P57790, P62993, P62994, P87379, Q05B84, Q07883, Q08012, Q13588, Q14145, Q16644, Q2T9Z7, Q3SYZ2, Q5PR73, Q5R4J7, Q5R6S2, Q5R774, Q5RKN4, Q5ZLD3, Q60631, Q66H84, Q66II3, Q684M4, Q6GPJ9, Q6TDP3, Q6YKA8, Q6ZPT1, Q7YRV6, Q861R0, Q8TC17

Diamond homologs: Q3ZCI3, Q5ZLT5, Q6P0G8, Q6P4L6, Q801R7, Q9D240, Q9NW61, D3ZL52, Q8BH49, Q8N4B1, A1CFB3, A1CYS1, A2CEA7, A2QNQ5, A7KAN4, B6RSP1, C4B4E5, O08967, O14827, O43739, P42331, P54644, P60669, P63034, P63035, P70392, P97694, P97696, Q00IB7, Q0CKU4, Q0UY53, Q14B98, Q15438, Q1RMU7, Q2KI41, Q2U0C3, Q4WID6, Q5B4C9, Q5U2Z7, Q6ICB4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

933 predictions. Top by Δscore:

Variant	Effect	Δscore
19:2233997:C:CA	donor_loss	1.0000
19:2234012:T:A	donor_gain	1.0000
19:2234024:T:A	donor_gain	1.0000
19:2234059:TAG:T	acceptor_gain	1.0000
19:2234062:C:CC	acceptor_gain	1.0000
19:2235760:A:AC	donor_gain	1.0000
19:2235761:C:CT	donor_gain	1.0000
19:2236154:CCG:C	donor_gain	1.0000
19:2233902:GGTCC:G	acceptor_loss	0.9900
19:2233906:C:CA	acceptor_loss	0.9900
19:2233906:C:CC	acceptor_gain	0.9900
19:2233907:T:A	acceptor_loss	0.9900
19:2234001:G:A	donor_gain	0.9900
19:2234056:TCGTA:T	acceptor_gain	0.9900
19:2234057:CGTAG:C	acceptor_gain	0.9900
19:2234058:GTAG:G	acceptor_gain	0.9900
19:2234060:AG:A	acceptor_gain	0.9900
19:2234061:GC:G	acceptor_loss	0.9900
19:2234162:AGAG:A	donor_gain	0.9900
19:2234240:CCT:C	acceptor_loss	0.9900
19:2234241:C:CC	acceptor_gain	0.9900
19:2234241:C:G	acceptor_loss	0.9900
19:2234242:T:G	acceptor_loss	0.9900
19:2235746:C:A	donor_gain	0.9900
19:2235757:CTCA:C	donor_gain	0.9900
19:2235761:CT:C	donor_gain	0.9900
19:2235761:CTG:C	donor_gain	0.9900
19:2235761:CTGA:C	donor_gain	0.9900
19:2235761:CTGAT:C	donor_gain	0.9900
19:2235785:T:TA	donor_gain	0.9900

AlphaMissense

975 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:2235947:G:C	F46L	0.999
19:2235947:G:T	F46L	0.999
19:2235949:A:G	F46L	0.999
19:2235956:A:C	N43K	0.999
19:2235956:A:T	N43K	0.999
19:2234175:A:G	W99R	0.998
19:2234175:A:T	W99R	0.998
19:2234207:A:G	F88S	0.998
19:2235948:A:G	F46S	0.998
19:2234173:C:A	W99C	0.997
19:2234173:C:G	W99C	0.997
19:2235764:A:T	I76N	0.997
19:2235818:G:T	A58D	0.997
19:2235827:G:T	P55H	0.997
19:2235951:A:T	L45H	0.997
19:2235966:A:G	L40P	0.997
19:2234038:A:G	L115P	0.996
19:2234047:C:G	R112P	0.996
19:2235815:A:G	L59P	0.996
19:2235946:A:C	Y47D	0.996
19:2235951:A:G	L45P	0.996
19:2235821:C:T	G57E	0.995
19:2235941:A:C	F48L	0.995
19:2235941:A:T	F48L	0.995
19:2235943:A:G	F48L	0.995
19:2235949:A:T	F46I	0.995
19:2235951:A:C	L45R	0.995
19:2235957:T:A	N43I	0.995
19:2236226:A:G	L8P	0.995
19:2234150:C:A	S107I	0.994

dbSNP variants (sampled 300 via entrez): RS1000189595 (19:2231792 C>G,T), RS1000622553 (19:2238022 G>C), RS1000720009 (19:2237005 G>C), RS1000978758 (19:2230011 A>G), RS1000979992 (19:2237137 G>A), RS1001011606 (19:2230177 G>C), RS1001237967 (19:2232123 G>A,T), RS1001289804 (19:2236120 C>G), RS1001607280 (19:2232241 C>G,T), RS1002208524 (19:2233149 C>A,T), RS1002287157 (19:2237002 C>A,G), RS1002359408 (19:2236739 C>A,G,T), RS1002396471 (19:2232339 A>C,T), RS1002710351 (19:2235525 A>G), RS1002871290 (19:2231487 C>G)

Disease associations

OMIM: gene MIM:617834 | 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
GCST003274_10	Pulse pressure	3.000000e-15
GCST90020027_190	Waist-hip index	8.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs740406	Efficacy	3	candesartan	Hypertension

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs740406	DOT1L, PLEKHJ1	3	3.00	1	candesartan

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, affects expression	2
Ozone	affects cotreatment, increases oxidation, increases abundance, affects expression	2
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
jinfukang	increases expression	1
Acetaminophen	affects response to substance	1
Acrolein	increases abundance, affects cotreatment, increases oxidation	1
Arsenic	affects methylation	1
Cadmium	increases abundance, increases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Selenium	increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
Vitamin E	increases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Acrylamide	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3E2	Abcam HEK293T PLEKHJ1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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