LRATD2

Summary

LRATD2 (LRAT domain containing 2, HGNC:24166) is a protein-coding gene on chromosome 8q24.21, encoding Protein LRATD2 (Q96KN1).

Located in cytoplasm and plasma membrane.

Source: NCBI Gene 157638 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 39 total — 1 pathogenic
• MANE Select transcript: NM_174911

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24166
Approved symbol	LRATD2
Name	LRAT domain containing 2
Location	8q24.21
Locus type	gene with protein product
Status	Approved
Aliases	BCMP101, NSE2
Ensembl gene	ENSG00000168672
Ensembl biotype	protein_coding
OMIM	609483
Entrez	157638

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000304916, ENST00000517458, ENST00000652209, ENST00000853985, ENST00000853987, ENST00000853988, ENST00000920140, ENST00000920141, ENST00000920142, ENST00000920143

RefSeq mRNA: 1 — MANE Select: NM_174911 NM_174911

CCDS: CCDS6358

Canonical transcript exons

ENST00000304916 — 2 exons

Exon	Start	End
ENSE00001124456	126552443	126557485
ENSE00001378219	126558034	126558478

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 99.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.0638 / max 3110.9665, expressed in 1125 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
94829	14.4820	1052
94832	7.5736	717
94824	2.4095	529
94831	2.3884	430
94830	0.6984	393
94828	0.4487	210
94819	0.2362	121
94823	0.1638	65
94822	0.1509	74
94820	0.1344	58

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	99.04	gold quality
pigmented layer of retina	UBERON:0001782	98.71	gold quality
secondary oocyte	CL:0000655	98.69	gold quality
retina	UBERON:0000966	98.68	gold quality
kidney epithelium	UBERON:0004819	98.47	gold quality
ventricular zone	UBERON:0003053	98.46	gold quality
renal medulla	UBERON:0000362	97.92	gold quality
eye	UBERON:0000970	97.55	gold quality
oocyte	CL:0000023	97.31	gold quality
palpebral conjunctiva	UBERON:0001812	97.19	gold quality
upper arm skin	UBERON:0004263	96.39	gold quality
epithelial cell of pancreas	CL:0000083	95.89	gold quality
oral cavity	UBERON:0000167	95.76	gold quality
buccal mucosa cell	CL:0002336	95.51	gold quality
oviduct epithelium	UBERON:0004804	94.89	gold quality
nasal cavity mucosa	UBERON:0001826	94.30	gold quality
lower esophagus mucosa	UBERON:0035834	94.16	gold quality
amniotic fluid	UBERON:0000173	94.05	gold quality
cortex of kidney	UBERON:0001225	94.04	gold quality
metanephros cortex	UBERON:0010533	94.02	gold quality
nasal cavity epithelium	UBERON:0005384	93.66	gold quality
kidney	UBERON:0002113	93.62	gold quality
ileal mucosa	UBERON:0000331	93.52	gold quality
adult mammalian kidney	UBERON:0000082	93.38	gold quality
germinal epithelium of ovary	UBERON:0001304	93.37	gold quality
cardiac muscle of right atrium	UBERON:0003379	93.27	gold quality
pharyngeal mucosa	UBERON:0000355	93.20	gold quality
cortical plate	UBERON:0005343	92.87	gold quality
esophagus squamous epithelium	UBERON:0006920	92.39	gold quality
saliva-secreting gland	UBERON:0001044	92.26	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-10287	yes	32.82
E-MTAB-7316	yes	20.12
E-ANND-3	yes	14.01
E-GEOD-81383	no	252.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

201 targeting LRATD2, 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-1252-5P	100.00	69.80	2774
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548P	99.98	72.25	3784
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-5696	99.98	72.36	4487
HSA-MIR-12136	99.98	72.81	5713

Literature-anchored findings (GeneRIF, showing 10)

• We demonstrated the decreased of circulating FAM84B mRNA and protein after neoadjuvant CRT may predict pCR, and FAM84B protein is overexpressed in ESCC. (PMID:25980316)
• Data suggest that FAM84B protein and the NOTCH pathway are involved in the progression of esophageal squamous cell carcinoma (ESCC) and may be potential diagnostic targets for ESCC susceptibility. (PMID:26759717)
• High FAM84B expression is associated with prostate cancer progression. (PMID:28186973)
• non-coding RNA (lncRNA) FAM84B-AS promotes resistance of Gastric Cancer to platinum drugs through inhibition of FAM84B expression. (PMID:30638658)
• The Oncogenic Potential of the Centromeric Border Protein FAM84B of the 8q24.21 Gene Desert. (PMID:32183428)
• FAM84B, amplified in pancreatic ductal adenocarcinoma, promotes tumorigenesis through the Wnt/beta-catenin pathway. (PMID:32291380)
• Identification of Hub Genes in Gastric Cancer with High Heterogeneity Based on Weighted Gene Co-Expression Network. (PMID:32558489)
• FAM84B acts as a tumor promoter in human glioma via affecting the Akt/GSK-3beta/beta-catenin pathway. (PMID:33759248)
• FAM84B promotes the proliferation of glioma cells through the cell cycle pathways. (PMID:36419094)
• FAM84B promotes breast cancer tumorigenesis through activation of the NF-kappaB and death receptor signaling pathways. (PMID:37651838)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	lratd2a	ENSDARG00000032859
danio_rerio	lratd2b	ENSDARG00000040280
mus_musculus	Lratd2	ENSMUSG00000072568
rattus_norvegicus	Lratd2	ENSRNOG00000004744

Paralogs (7): LRAT (ENSG00000121207), PLAAT1 (ENSG00000127252), PLAAT4 (ENSG00000133321), PLAAT2 (ENSG00000133328), LRATD1 (ENSG00000162981), PLAAT5 (ENSG00000168004), PLAAT3 (ENSG00000176485)

Protein

Protein identifiers

Protein LRATD2 — Q96KN1 (reviewed: Q96KN1)

Alternative names: Breast cancer membrane protein 101, LRAT domain-containing 2, Protein FAM84B, Protein NSE2

All UniProt accessions (1): Q96KN1

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed in esophageal squamous cell carcinomas.

Similarity. Belongs to the LRATD family.

RefSeq proteins (1): NP_777571* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007053	LRAT_dom	Domain
IPR043299	LRATD1_LRATD2	Family

Pfam: PF04970

UniProt features (8 total): compositionally biased region 4, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KN1-F1	78.97	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 214 (showing top): TAATAAT_MIR126, TTTGTAG_MIR520D, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, ATGTTAA_MIR302C, IRF7_01, TGCTGAY_UNKNOWN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, TTGGAGA_MIR5155P_MIR519E, AACTTT_UNKNOWN, DOUGLAS_BMI1_TARGETS_UP, EGR1_01, ACEVEDO_LIVER_CANCER_UP, RIGGI_EWING_SARCOMA_PROGENITOR_UP

GO Biological Process (0):

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

GO Cellular Component (2): cytoplasm (GO:0005737), plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

632 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRATD2	CTNNA1	P35221	693
LRATD2	POU5F1B	Q06416	642
LRATD2	GSDMC	Q9BYG8	595
LRATD2	PLAAT1	Q9HDD0	595
LRATD2	CLBA1	Q96F83	507
LRATD2	PLAAT2	Q9NWW9	496
LRATD2	ZNF572	Q7Z3I7	448
LRATD2	VWA5B2	Q8N398	429
LRATD2	DIPK2B	Q9H7Y0	428
LRATD2	E7ENQ6	E7ENQ6	420
LRATD2	WDR81	Q562E7	419
LRATD2	LRWD1	Q9UFC0	418
LRATD2	ECPAS	Q5VYK3	405
LRATD2	HRAS	P01112	404
LRATD2	CZIB	Q9NWV4	392

IntAct

48 interactions, top by confidence:

A	B	Type	Score
LRATD2	UROD	psi-mi:“MI:0915”(physical association)	0.780
UROD	LRATD2	psi-mi:“MI:0915”(physical association)	0.780
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
LRATD2	NMT2	psi-mi:“MI:0915”(physical association)	0.640
LRATD2	NMT2	psi-mi:“MI:0914”(association)	0.640
TAX1BP1	LRATD2	psi-mi:“MI:0915”(physical association)	0.560
DDIT4L	LRATD2	psi-mi:“MI:0915”(physical association)	0.560
LRATD2	AP1M1	psi-mi:“MI:0915”(physical association)	0.560
LRATD2	RAD51	psi-mi:“MI:0915”(physical association)	0.540
RAD51	LRATD2	psi-mi:“MI:0915”(physical association)	0.540
CHEK2	LRATD2	psi-mi:“MI:0915”(physical association)	0.540
LRATD2	RAD51	psi-mi:“MI:0403”(colocalization)	0.540
LRATD2	CHEK2	psi-mi:“MI:0403”(colocalization)	0.540
GDE1	GAPDHS	psi-mi:“MI:0914”(association)	0.530
IZUMO1	ADCY3	psi-mi:“MI:0914”(association)	0.530
LRATD2	ADRB2	psi-mi:“MI:0915”(physical association)	0.370
BAG4	LRATD2	psi-mi:“MI:0915”(physical association)	0.370
LRATD2	ESR2	psi-mi:“MI:0915”(physical association)	0.370
FGFR4	LRATD2	psi-mi:“MI:0915”(physical association)	0.370
NOTCH2	LRATD2	psi-mi:“MI:0915”(physical association)	0.370
PALB2	LRATD2	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (46): FAM84B (Two-hybrid), NMT1 (Affinity Capture-MS), NMT2 (Affinity Capture-MS), EIF1AX (Affinity Capture-MS), FAM84B (Affinity Capture-MS), FAM84B (Affinity Capture-MS), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid), FAM84B (Two-hybrid)

ESM2 similar proteins: A0A0R4IMY7, A0A0R4IY06, A0JPF9, A2AP18, A5PJN5, C0IN03, D2KX21, E1BVR9, E9PYK3, F1ND48, O00534, O75038, O94952, O95237, P0C1Q3, P53817, Q1LWG4, Q1LZ50, Q32PY6, Q4R3W5, Q4R6L3, Q5M7X9, Q5R5S1, Q5RJG7, Q5S6T3, Q5T8I9, Q6DC39, Q75WE7, Q7Z5M8, Q7ZU92, Q8BYI6, Q8C0L6, Q8CAE2, Q8CAS9, Q8K3R3, Q8NHH9, Q8SPR7, Q8VDH1, Q90678, Q93V51

Diamond homologs: Q3ZCA1, Q96KN1, Q96KN4, Q9D650, P53816, Q5R611, Q8R3U1, Q9NWW9, Q9QZU4, A0A0R4IY06, D2KX21, O95237, P53817, Q4KLN5, Q96KN8, Q9BGL2, Q9CPX5, Q9HDD0, Q9JI60, Q9JI61, Q9UL19

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	35
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
625635	GRCh37/hg19 8q24.13-24.21(chr8:127185755-128672802)	Pathogenic

SpliceAI

413 predictions. Top by Δscore:

Variant	Effect	Δscore
8:126558027:AACT:A	donor_loss	0.9800
8:126558028:AC:A	donor_loss	0.9800
8:126558029:CTCA:C	donor_loss	0.9800
8:126558032:A:AC	donor_gain	0.9800
8:126558032:A:G	donor_loss	0.9800
8:126558033:C:CC	donor_gain	0.9800
8:126558033:CCCG:C	donor_gain	0.9800
8:126558026:AAAC:A	donor_loss	0.9700
8:126558032:AC:A	donor_gain	0.9700
8:126558033:CC:C	donor_gain	0.9700
8:126553501:TTCC:T	acceptor_loss	0.9600
8:126553502:TCC:T	acceptor_loss	0.9600
8:126553504:CTA:C	acceptor_loss	0.9600
8:126553505:T:A	acceptor_loss	0.9600
8:126556448:G:C	donor_gain	0.9500
8:126557417:C:CT	acceptor_gain	0.9500
8:126556470:G:GA	donor_gain	0.9300
8:126553504:C:CC	acceptor_gain	0.9200
8:126556452:G:A	donor_gain	0.9100
8:126556482:T:TA	donor_gain	0.8900
8:126556485:T:TA	donor_gain	0.8900
8:126553506:A:C	acceptor_loss	0.8700
8:126556413:A:AC	donor_gain	0.8700
8:126556414:C:CC	donor_gain	0.8700
8:126558093:T:TA	donor_gain	0.8700
8:126556479:T:TA	donor_gain	0.8600
8:126553501:TTC:T	acceptor_gain	0.8500
8:126558073:C:CA	donor_gain	0.8400
8:126556551:T:TA	donor_gain	0.8300
8:126557483:TACC:T	acceptor_loss	0.8300

AlphaMissense

2019 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:126556658:G:C	F244L	1.000
8:126556658:G:T	F244L	1.000
8:126556659:A:G	F244S	1.000
8:126556660:A:G	F244L	1.000
8:126556708:A:C	Y228D	1.000
8:126556746:A:G	F215S	1.000
8:126556779:A:G	F204S	1.000
8:126556798:A:G	W198R	1.000
8:126556798:A:T	W198R	1.000
8:126557276:G:C	F38L	1.000
8:126557276:G:T	F38L	1.000
8:126557278:A:G	F38L	1.000
8:126556623:C:G	R256P	0.999
8:126556626:C:G	R255P	0.999
8:126556641:A:G	L250P	0.999
8:126556660:A:C	F244V	0.999
8:126556660:A:T	F244I	0.999
8:126556701:A:G	L230P	0.999
8:126556742:C:A	K216N	0.999
8:126556742:C:G	K216N	0.999
8:126556745:G:C	F215L	0.999
8:126556745:G:T	F215L	0.999
8:126556747:A:G	F215L	0.999
8:126556766:G:C	C208W	0.999
8:126556768:A:G	C208R	0.999
8:126556771:A:G	W207R	0.999
8:126556771:A:T	W207R	0.999
8:126556776:G:T	A205D	0.999
8:126556778:G:C	F204L	0.999
8:126556778:G:T	F204L	0.999

dbSNP variants (sampled 300 via entrez): RS1000135662 (8:126552183 G>T), RS1000238845 (8:126557169 T>C), RS1000287982 (8:126556702 G>A), RS1001581450 (8:126558659 C>T), RS1002023373 (8:126552718 T>C), RS1002100164 (8:126556089 G>A,T), RS1002534720 (8:126556441 G>A,T), RS1003130649 (8:126554862 T>A,C), RS1003169278 (8:126556032 C>T), RS1003204702 (8:126559680 T>C), RS1003256967 (8:126560061 C>G,T), RS1003489209 (8:126555224 T>G), RS1003833608 (8:126554519 G>A), RS1004035986 (8:126553523 A>G), RS1004224036 (8:126557789 G>C,T)

Disease associations

OMIM: gene MIM:609483 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001762_377	Obesity-related traits	8.000000e-06
GCST001762_891	Obesity-related traits	4.000000e-07
GCST001814_16	Age-related macular degeneration	5.000000e-06
GCST004863_22	Mosquito bite size	2.000000e-07
GCST005790_15	Rosacea symptom severity	6.000000e-06
GCST008062_54	Blood urea nitrogen levels	3.000000e-20
GCST009391_482	Metabolite levels	6.000000e-06
GCST010479_9	Coronary artery disease	5.000000e-10
GCST90011900_202	Serum alkaline phosphatase levels	2.000000e-149

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0008378	mosquito bite reaction size measurement
EFO:0009180	rosacea severity measurement
EFO:0010389	phosphatidylcholine 40:6 measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
trichostatin A	affects cotreatment, decreases expression	3
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Zoledronic Acid	decreases expression	2
Cisplatin	affects cotreatment, increases expression	2
Estradiol	affects cotreatment, decreases expression	2
Smoke	decreases expression	2
Particulate Matter	increases abundance, increases expression, affects cotreatment	2
FR900359	affects phosphorylation	1
sotorasib	affects cotreatment, decreases expression	1
tungsten carbide	affects cotreatment, decreases expression	1
chloroacetaldehyde	increases expression	1
arsenite	affects binding, decreases reaction	1
tobacco tar	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
potassium chromate(VI)	increases expression	1
cupric chloride	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
trametinib	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases reaction, increases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Cidofovir	increases expression	1
Air Pollutants	increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E0GP	Ubigene HeLa LRATD2 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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