ODR4

Summary

ODR4 (odr-4 GPCR localization factor homolog, HGNC:24299) is a protein-coding gene on chromosome 1q31.1, encoding Protein odr-4 homolog (Q5SWX8). May play a role in the trafficking of a subset of G-protein coupled receptors. It is a selective cancer dependency (DepMap: 18.5% of cell lines).

Predicted to be involved in protein localization. Predicted to be located in membrane.

Source: NCBI Gene 54953 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 25 total
• Cancer dependency (DepMap): dependent in 18.5% of screened cell lines
• MANE Select transcript: NM_017847

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24299
Approved symbol	ODR4
Name	odr-4 GPCR localization factor homolog
Location	1q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20505, odr-4, TTG1
Ensembl gene	ENSG00000157181
Ensembl biotype	protein_coding
OMIM	609335
Entrez	54953

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 11 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000287859, ENST00000367470, ENST00000419367, ENST00000461662, ENST00000478571, ENST00000871092, ENST00000969392, ENST00000969393, ENST00000969394, ENST00000969395, ENST00000969396, ENST00000969397, ENST00000969398

RefSeq mRNA: 3 — MANE Select: NM_017847 NM_001164245, NM_001164246, NM_017847

CCDS: CCDS53448, CCDS53449, CCDS53450

Canonical transcript exons

ENST00000287859 — 14 exons

Exon	Start	End
ENSE00001068234	186389588	186389624
ENSE00001068236	186379767	186379884
ENSE00001068237	186398313	186398441
ENSE00001068238	186383022	186383156
ENSE00001068239	186385988	186386083
ENSE00001068241	186388442	186388548
ENSE00001068242	186391696	186391791
ENSE00001068243	186393947	186394015
ENSE00001068244	186390711	186390851
ENSE00001126065	186417544	186417654
ENSE00001872260	186375838	186375974
ENSE00003544641	186398954	186399044
ENSE00003627566	186406083	186406268
ENSE00003844831	186419009	186421375

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 93.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1946 / max 258.3651, expressed in 1775 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
7359	13.5039	1768
7358	1.0010	498
7357	0.6898	266

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	93.29	gold quality
calcaneal tendon	UBERON:0003701	93.24	gold quality
caput epididymis	UBERON:0004358	92.66	gold quality
tendon of biceps brachii	UBERON:0008188	92.19	gold quality
tendon	UBERON:0000043	92.11	gold quality
adrenal tissue	UBERON:0018303	91.85	gold quality
body of pancreas	UBERON:0001150	91.54	gold quality
corpus callosum	UBERON:0002336	90.85	gold quality
cauda epididymis	UBERON:0004360	90.83	gold quality
parotid gland	UBERON:0001831	90.42	gold quality
cardia of stomach	UBERON:0001162	90.09	gold quality
pericardium	UBERON:0002407	89.63	gold quality
cartilage tissue	UBERON:0002418	89.20	gold quality
lower lobe of lung	UBERON:0008949	88.97	gold quality
pancreas	UBERON:0001264	88.65	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.35	gold quality
buccal mucosa cell	CL:0002336	88.25	gold quality
amniotic fluid	UBERON:0000173	88.03	gold quality
superior surface of tongue	UBERON:0007371	87.80	gold quality
adenohypophysis	UBERON:0002196	87.74	gold quality
mammary duct	UBERON:0001765	87.68	gold quality
trigeminal ganglion	UBERON:0001675	87.58	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.49	gold quality
inferior vagus X ganglion	UBERON:0005363	87.38	gold quality
right lobe of liver	UBERON:0001114	87.33	gold quality
seminal vesicle	UBERON:0000998	87.04	gold quality
endometrium	UBERON:0001295	87.00	gold quality
pituitary gland	UBERON:0000007	86.76	gold quality
saliva-secreting gland	UBERON:0001044	86.72	gold quality
lower esophagus mucosa	UBERON:0035834	86.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	216.40
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting ODR4, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-656-3P	100.00	72.15	2788
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-5696	99.98	72.36	4487
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-95-5P	99.89	72.17	3973

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 18.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

• LMO2, TAL1, Ttg-1, and SIL support levels of V(D)J recombination above background levels in cell culture and are also cleaved by the RAG proteins, while Hox11 and SCL are nicked but not cleaved efficiently in vitro (PMID:18187418)
• Human C1orf27 protein interacts with alpha2A-adrenergic receptor and regulates its anterograde transport. (PMID:35551911)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	odr4	ENSDARG00000042671
mus_musculus	Odr4	ENSMUSG00000006010
rattus_norvegicus	Odr4	ENSRNOG00000002473

Protein

Protein identifiers

Protein odr-4 homolog — Q5SWX8 (reviewed: Q5SWX8)

Alternative names: LAG1-interacting protein, Transactivated by transforming growth factor beta protein 1

All UniProt accessions (1): Q5SWX8

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the trafficking of a subset of G-protein coupled receptors.

Subcellular location. Membrane.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the ODR-4 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q5SWX8-1	1	yes
Q5SWX8-2	2
Q5SWX8-3	3
Q5SWX8-4	4

RefSeq proteins (3): NP_001157717, NP_001157718, NP_060317* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029454	ODR-4-like	Family

Pfam: PF14778

UniProt features (13 total): sequence conflict 5, splice variant 4, transmembrane region 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SWX8-F1	80.69	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 126 (showing top): PAX4_01, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GGAMTNNNNNTCCY_UNKNOWN, ONKEN_UVEAL_MELANOMA_UP, KONDO_COLON_CANCER_HCP_WITH_H3K27ME1, CREB_Q3, PARENT_MTOR_SIGNALING_UP, YGCGYRCGC_UNKNOWN, CHEN_HOXA5_TARGETS_9HR_UP, SMAD_Q6, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP, CHEN_LIVER_METABOLISM_QTL_CIS, JOHNSTONE_PARVB_TARGETS_3_DN, FEVR_CTNNB1_TARGETS_UP, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP

GO Biological Process (1): intracellular protein localization (GO:0008104)

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
macromolecule localization	1
cellular anatomical structure	1

Protein interactions and networks

STRING

324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ODR4	UFSP2	Q9NUQ7	529
ODR4	RTP2	Q5QGT7	528
ODR4	RTP1	P59025	479
ODR4	UFSP1	Q6NVU6	449
ODR4	CFAP210	Q0VFZ6	447
ODR4	TXNL1	O43396	443
ODR4	AGPS	O00116	443
ODR4	Q4G0F9	Q4G0F9	415
ODR4	DNAJC14	Q6Y2X3	403
ODR4	AP5Z1	O43299	392
ODR4	DPM1	O60762	377
ODR4	DDRGK1	Q96HY6	372
ODR4	SEC13	P55735	349
ODR4	UBA5	Q9GZZ9	349
ODR4	BTD	P43251	343

IntAct

127 interactions, top by confidence:

A	B	Type	Score
DDRGK1	UFL1	psi-mi:“MI:0914”(association)	0.710
CD27	TCAF2	psi-mi:“MI:0914”(association)	0.640
LRATD2	NMT2	psi-mi:“MI:0914”(association)	0.640
SLC1A1	AGPAT2	psi-mi:“MI:0914”(association)	0.640
BTN3A2	BTN3A1	psi-mi:“MI:0914”(association)	0.600
BTN3A3	BTN3A1	psi-mi:“MI:0914”(association)	0.560
GRB2	SH3PXD2B	psi-mi:“MI:0914”(association)	0.530
CD79A	METTL15	psi-mi:“MI:0914”(association)	0.530
TMX1	NRP1	psi-mi:“MI:0914”(association)	0.530
FAM177A1	SLC27A2	psi-mi:“MI:0914”(association)	0.530
IL27RA	B4GALT5	psi-mi:“MI:0914”(association)	0.530
NAPA	NBAS	psi-mi:“MI:0914”(association)	0.530
ILVBL	SLC33A1	psi-mi:“MI:0914”(association)	0.530
DLK1	SCAMP3	psi-mi:“MI:0914”(association)	0.530
CD244	MTX2	psi-mi:“MI:0914”(association)	0.530
LRIG1	LRIG2	psi-mi:“MI:0914”(association)	0.530
ARFGAP1	AURKA	psi-mi:“MI:0914”(association)	0.530
CD79A	ODR4	psi-mi:“MI:0914”(association)	0.530
CLCC1	PLSCR1	psi-mi:“MI:0914”(association)	0.530
EVA1C	STK25	psi-mi:“MI:0914”(association)	0.530
GPRC5B	STXBP3	psi-mi:“MI:0914”(association)	0.530
LRRTM4	AP3B1	psi-mi:“MI:0914”(association)	0.530
SLC25A6	HRAS	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
ATM	RBM47	psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
	DENND11	psi-mi:“MI:0914”(association)	0.350
M	DENND11	psi-mi:“MI:0914”(association)	0.350

BioGRID (136): C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-Western), UFSP2 (Co-localization), C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Proximity Label-MS), C1orf27 (Proximity Label-MS), C1orf27 (Affinity Capture-MS), C1orf27 (Proximity Label-MS), C1orf27 (Affinity Capture-MS)

ESM2 similar proteins: A0JMA8, A0JPP5, A1A535, A1A5P5, F1S5L4, O70481, P86790, P86791, P97564, Q008S8, Q0VA04, Q0VD30, Q14D04, Q16K67, Q19317, Q28HU2, Q2KI89, Q3KQ18, Q45GW3, Q4R6I5, Q4S4I5, Q5GJ77, Q5PQS3, Q5R629, Q5R6E9, Q5RD58, Q5SWX8, Q5U245, Q5XIR8, Q5ZKK3, Q5ZLN2, Q61586, Q6NU25, Q6PA97, Q7Z3E5, Q803R2, Q86VS3, Q8C1Y8, Q8CDK3, Q8IWV7

Diamond homologs: A3KNB6, Q0VA36, Q4PJX1, Q5R6E9, Q5SWX8, Q5ZKH8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 181 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
Signaling by FLT3 ITD and TKD mutants	5	36.6×	1e-04
DAP12 signaling	5	17.7×	3e-04
NCAM signaling for neurite out-growth	5	13.1×	7e-04
Protein localization	5	9.2×	2e-03
Membrane Trafficking	10	3.6×	5e-03
Vesicle-mediated transport	10	3.4×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of type II interferon production	7	10.2×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2401 predictions. Top by Δscore:

Variant	Effect	Δscore
1:186375972:CAGGT:C	donor_loss	1.0000
1:186375973:AGGTA:A	donor_loss	1.0000
1:186375976:T:A	donor_loss	1.0000
1:186379759:T:TA	acceptor_gain	1.0000
1:186379766:GGA:G	acceptor_gain	1.0000
1:186379882:CAGGT:C	donor_loss	1.0000
1:186379883:AGG:A	donor_loss	1.0000
1:186379884:GGTA:G	donor_loss	1.0000
1:186379885:G:T	donor_loss	1.0000
1:186379886:T:A	donor_loss	1.0000
1:186386079:GTAGA:G	donor_gain	1.0000
1:186386082:GA:G	donor_gain	1.0000
1:186386084:G:GG	donor_gain	1.0000
1:186388502:G:GT	donor_gain	1.0000
1:186388549:G:GG	donor_gain	1.0000
1:186388571:TTTAA:T	donor_gain	1.0000
1:186389577:A:AG	acceptor_gain	1.0000
1:186389581:A:AG	acceptor_gain	1.0000
1:186389582:G:GG	acceptor_gain	1.0000
1:186390710:GA:G	acceptor_gain	1.0000
1:186391689:T:A	acceptor_gain	1.0000
1:186391693:A:AG	acceptor_gain	1.0000
1:186391694:A:AG	acceptor_gain	1.0000
1:186391694:AGAAT:A	acceptor_gain	1.0000
1:186391695:G:GG	acceptor_gain	1.0000
1:186391695:GAATG:G	acceptor_gain	1.0000
1:186391791:GGTA:G	donor_loss	1.0000
1:186391792:G:A	donor_loss	1.0000
1:186391793:T:G	donor_loss	1.0000
1:186394012:GTTG:G	donor_gain	1.0000

AlphaMissense

3000 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:186390732:T:A	W166R	0.995
1:186390732:T:C	W166R	0.995
1:186379880:G:A	G32E	0.991
1:186398991:G:C	R316P	0.990
1:186379871:T:C	L29P	0.987
1:186386001:T:C	L83P	0.987
1:186386024:G:A	G91R	0.985
1:186386024:G:C	G91R	0.985
1:186386025:G:A	G91E	0.984
1:186388524:T:C	L138P	0.984
1:186390727:C:A	A164E	0.984
1:186383053:C:A	A44D	0.982
1:186389599:G:C	R150P	0.982
1:186379868:G:A	G28D	0.981
1:186379874:T:C	L30S	0.981
1:186379879:G:A	G32R	0.981
1:186379879:G:C	G32R	0.981
1:186379798:T:G	Y5D	0.980
1:186383044:T:A	V41E	0.980
1:186383148:G:C	A76P	0.980
1:186390762:T:A	W176R	0.980
1:186390762:T:C	W176R	0.980
1:186398391:T:C	C287R	0.980
1:186379794:A:C	R3S	0.979
1:186379794:A:T	R3S	0.979
1:186386025:G:T	G91V	0.979
1:186390726:G:C	A164P	0.979
1:186398398:C:A	A289D	0.977
1:186386030:T:C	F93L	0.976
1:186386032:T:A	F93L	0.976

dbSNP variants (sampled 300 via entrez): RS1000085484 (1:186392745 G>C,T), RS1000113607 (1:186400913 C>T), RS1000116726 (1:186392972 T>C), RS1000169648 (1:186374028 G>A), RS1000274946 (1:186416438 A>G), RS1000306255 (1:186416681 A>C), RS1000309223 (1:186425063 T>C), RS1000335736 (1:186383587 ATTTTC>A), RS1000367947 (1:186386384 T>C), RS1000391892 (1:186376550 C>A), RS1000394516 (1:186380545 G>A,C,T), RS1000441117 (1:186412652 T>A), RS1000447782 (1:186422005 A>G), RS1000464904 (1:186399558 T>C,G), RS1000538558 (1:186417886 TAAAAG>T)

Disease associations

OMIM: gene MIM:609335 | 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

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	3
Air Pollutants	increases abundance, increases oxidation, increases expression, affects cotreatment	2
Particulate Matter	increases abundance, increases expression	2
dicrotophos	decreases expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
sodium arsenite	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
epigallocatechin gallate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	increases expression	1
jinfukang	decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, increases expression	1
Leflunomide	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Vehicle Emissions	increases abundance, increases expression	1
Benzo(a)pyrene	increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Gallic Acid	decreases expression	1
Gold	decreases expression	1
Ivermectin	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	increases expression	1
Valproic Acid	decreases methylation	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Isotretinoin	decreases expression	1
Cadmium Chloride	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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