LRATD1

Summary

LRATD1 (LRAT domain containing 1, HGNC:20743) is a protein-coding gene on chromosome 2p24.3, encoding Protein LRATD1 (Q96KN4). May play a role in cell morphology and motility.

Involved in cell morphogenesis and cell motility. Predicted to be located in cytoplasm.

Source: NCBI Gene 151354 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 36 total — 1 likely-pathogenic
• MANE Select transcript: NM_145175

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20743
Approved symbol	LRATD1
Name	LRAT domain containing 1
Location	2p24.3
Locus type	gene with protein product
Status	Approved
Aliases	NSE1, FLJ35392
Ensembl gene	ENSG00000162981
Ensembl biotype	protein_coding
OMIM	611234
Entrez	151354

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 16 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000295092, ENST00000331243, ENST00000464947, ENST00000497769, ENST00000851919, ENST00000851920, ENST00000851921, ENST00000851922, ENST00000851923, ENST00000851924, ENST00000851925, ENST00000851926, ENST00000851927, ENST00000851928, ENST00000851929, ENST00000851930, ENST00000851931, ENST00000961730

RefSeq mRNA: 2 — MANE Select: NM_145175 NM_001369364, NM_145175

CCDS: CCDS1684

Canonical transcript exons

ENST00000295092 — 2 exons

Exon	Start	End
ENSE00001070322	14633944	14640041
ENSE00001070323	14632717	14632937

Expression profiles

Bgee: expression breadth ubiquitous, 226 present calls, max score 99.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.8901 / max 383.4735, expressed in 1016 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18962	8.5312	941
18964	0.7776	465
18963	0.4174	205
18961	0.1107	53
18965	0.0532	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	99.37	gold quality
ileum	UBERON:0002116	99.27	silver quality
corpus epididymis	UBERON:0004359	97.99	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.94	gold quality
colonic mucosa	UBERON:0000317	97.48	gold quality
rectum	UBERON:0001052	96.33	gold quality
upper arm skin	UBERON:0004263	96.22	gold quality
endothelial cell	CL:0000115	96.05	gold quality
buccal mucosa cell	CL:0002336	95.19	gold quality
gingiva	UBERON:0001828	94.85	gold quality
gingival epithelium	UBERON:0001949	94.57	gold quality
nasal cavity epithelium	UBERON:0005384	94.43	gold quality
mammalian vulva	UBERON:0000997	93.36	gold quality
mucosa of transverse colon	UBERON:0004991	93.12	gold quality
middle temporal gyrus	UBERON:0002771	92.82	gold quality
jejunal mucosa	UBERON:0000399	92.66	gold quality
Brodmann (1909) area 23	UBERON:0013554	92.40	gold quality
upper leg skin	UBERON:0004262	92.35	gold quality
esophagus squamous epithelium	UBERON:0006920	92.13	gold quality
penis	UBERON:0000989	91.95	gold quality
superior frontal gyrus	UBERON:0002661	91.88	gold quality
primary visual cortex	UBERON:0002436	91.82	gold quality
bronchial epithelial cell	CL:0002328	91.62	gold quality
caput epididymis	UBERON:0004358	91.31	gold quality
bronchus	UBERON:0002185	91.20	gold quality
lower esophagus mucosa	UBERON:0035834	91.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.02	gold quality
esophagus mucosa	UBERON:0002469	90.96	gold quality
duodenum	UBERON:0002114	90.47	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.39	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	63.98
E-HCAD-10	yes	40.30
E-MTAB-5061	yes	25.57
E-GEOD-81608	yes	17.72
E-ENAD-27	yes	9.49
E-GEOD-83139	yes	9.42
E-ANND-3	yes	9.05

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I3

miRNA regulators (miRDB)

209 targeting LRATD1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-548AA	99.96	70.64	3753

Literature-anchored findings (GeneRIF, showing 2)

• up-regulation of FAM84A may play a critical role in progression of colon cancer (PMID:16820875)
• The direct miR-874-3p-target FAM84A promotes tumor development in papillary thyroid cancer. (PMID:33751775)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lratd1	ENSDARG00000018921
mus_musculus	Lratd1	ENSMUSG00000020607
rattus_norvegicus	Lratd1	ENSRNOG00000004084

Paralogs (7): LRAT (ENSG00000121207), PLAAT1 (ENSG00000127252), PLAAT4 (ENSG00000133321), PLAAT2 (ENSG00000133328), PLAAT5 (ENSG00000168004), LRATD2 (ENSG00000168672), PLAAT3 (ENSG00000176485)

Protein

Protein identifiers

Protein LRATD1 — Q96KN4 (reviewed: Q96KN4)

Alternative names: LRAT domain-containing 1, Neurologic sensory protein 1, Protein FAM84A

All UniProt accessions (1): Q96KN4

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cell morphology and motility.

Subcellular location. Cytoplasm.

Tissue specificity. Only detected in testis. Highly expressed in colon cancer cells.

Similarity. Belongs to the LRATD family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96KN4-1	1	yes
Q96KN4-2	2

RefSeq proteins (2): NP_001356293, NP_660158* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007053	LRAT_dom	Domain
IPR043299	LRATD1_LRATD2	Family

Pfam: PF04970

UniProt features (8 total): mutagenesis site 2, sequence conflict 2, chain 1, domain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KN4-F1	77.23	0.45

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 (1): 38

Mutagenesis-validated functional residues (2):

Position	Phenotype
38	abolishes phosphorylation.
67	no effect on phosphorylation.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 141 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, RNGTGGGC_UNKNOWN, BENPORATH_ES_WITH_H3K27ME3, MYOGENIN_Q6, GOZGIT_ESR1_TARGETS_DN, RACCACAR_AML_Q6, AML_Q6, TGCTGAY_UNKNOWN, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, LASTOWSKA_COAMPLIFIED_WITH_MYCN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, LINDVALL_IMMORTALIZED_BY_TERT_DN, RIGGI_EWING_SARCOMA_PROGENITOR_UP, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, OSF2_Q6

GO Biological Process (2): cell morphogenesis (GO:0000902), cell motility (GO:0048870)

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

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
anatomical structure morphogenesis	1
cellular process	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

420 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRATD1	CYRIA	Q9H0Q0	560
LRATD1	PPP1R1A	Q13522	467
LRATD1	NT5DC2	Q9H857	462
LRATD1	ANKRD55	Q3KP44	455
LRATD1	PLAAT1	Q9HDD0	455
LRATD1	SF3B3	Q15393	453
LRATD1	CZIB	Q9NWV4	425
LRATD1	GARRE1	O15063	425
LRATD1	RSAD1	Q9HA92	406
LRATD1	RESF1	Q9HCM1	402
LRATD1	PLAAT2	Q9NWW9	401
LRATD1	ZNF415	Q09FC8	396
LRATD1	PLAAT5	Q96KN8	393
LRATD1	DOP1A	Q5JWR5	390
LRATD1	DUSP15	Q9H1R2	387

IntAct

14 interactions, top by confidence:

A	B	Type	Score
CYGB	LRATD1	psi-mi:“MI:0915”(physical association)	0.560
ARHGEF5	LRATD1	psi-mi:“MI:0915”(physical association)	0.560
ATXN10	LRATD1	psi-mi:“MI:0915”(physical association)	0.560
	LRATD1	psi-mi:“MI:0915”(physical association)	0.400
LRATD1	NMT2	psi-mi:“MI:0914”(association)	0.350
CYGB	LRATD1	psi-mi:“MI:0915”(physical association)	0.000
ARHGEF5	LRATD1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): FAM84A (Two-hybrid), FAM84A (Two-hybrid), FIGNL1 (Affinity Capture-MS), NMT2 (Affinity Capture-MS), NMT1 (Affinity Capture-MS), FAM84A (Cross-Linking-MS (XL-MS)), FAM84A (Affinity Capture-Luminescence)

ESM2 similar proteins: A1L1C2, A2RRU4, A6QM06, A6QP75, E1BE10, E2RD63, G5E872, O75888, P29376, P70295, P97260, Q12770, Q1LZ97, Q28DT3, Q2M2I3, Q3TAA7, Q3U5Q7, Q3ZCA1, Q4FZD7, Q5EBM0, Q5MNU5, Q5SWZ9, Q60I26, Q60I27, Q69Z89, Q6AZ51, Q6GQT6, Q6IN84, Q6NUI2, Q6P9U1, Q7Z6J9, Q8BH06, Q8BTM9, Q8C0R7, Q8IYL2, Q8N1F8, Q8N2A8, Q8NAC3, Q8NFR9, Q8TDF6

Diamond homologs: Q3ZCA1, Q96KN1, Q96KN4, Q9D650, P53816, Q5R611, Q8R3U1, Q9NWW9, Q9QZU4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	34
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1675850	GRCh37/hg19 2p24.3(chr2:14774068-15679480)x1	Likely pathogenic

SpliceAI

1200 predictions. Top by Δscore:

Variant	Effect	Δscore
2:14632904:G:GT	donor_gain	1.0000
2:14633938:CCGCA:C	acceptor_loss	1.0000
2:14633939:CGCA:C	acceptor_loss	1.0000
2:14633940:GCAGA:G	acceptor_loss	1.0000
2:14633941:CAG:C	acceptor_loss	1.0000
2:14633942:A:AG	acceptor_gain	1.0000
2:14633942:A:C	acceptor_loss	1.0000
2:14633943:G:GA	acceptor_gain	1.0000
2:14632849:G:GT	donor_gain	0.9900
2:14632893:G:GT	donor_gain	0.9900
2:14632894:A:T	donor_gain	0.9900
2:14632905:GAGTT:G	donor_gain	0.9900
2:14632928:G:T	donor_gain	0.9900
2:14633933:T:TA	acceptor_gain	0.9900
2:14633943:GA:G	acceptor_gain	0.9900
2:14633943:GAT:G	acceptor_gain	0.9900
2:14633943:GATC:G	acceptor_gain	0.9900
2:14633943:GATCC:G	acceptor_gain	0.9900
2:14632904:GGA:G	donor_gain	0.9800
2:14632906:A:T	donor_gain	0.9800
2:14633839:G:GG	donor_gain	0.9800
2:14633931:T:TA	acceptor_gain	0.9800
2:14633939:C:CA	acceptor_gain	0.9800
2:14635602:G:T	donor_gain	0.9800
2:14635624:G:GT	donor_gain	0.9800
2:14635645:G:GG	donor_gain	0.9800
2:14649108:G:GG	donor_gain	0.9800
2:14649118:C:G	donor_gain	0.9800
2:14633824:C:G	donor_gain	0.9700
2:14632920:G:GT	donor_gain	0.9600

AlphaMissense

1904 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:14634604:T:A	W209R	1.000
2:14634604:T:C	W209R	1.000
2:14634623:T:C	F215S	1.000
2:14634656:T:C	F226S	1.000
2:14634660:G:C	K227N	1.000
2:14634660:G:T	K227N	1.000
2:14633983:G:C	G2R	0.999
2:14634002:T:C	I8T	0.999
2:14634016:T:C	Y13H	0.999
2:14634088:T:C	F37L	0.999
2:14634090:C:A	F37L	0.999
2:14634090:C:G	F37L	0.999
2:14634242:C:A	A88D	0.999
2:14634347:G:A	G123D	0.999
2:14634347:G:T	G123V	0.999
2:14634353:T:C	L125P	0.999
2:14634409:T:A	W144R	0.999
2:14634409:T:C	W144R	0.999
2:14634416:T:A	V146D	0.999
2:14634566:C:A	A196D	0.999
2:14634605:G:C	W209S	0.999
2:14634606:G:C	W209C	0.999
2:14634606:G:T	W209C	0.999
2:14634622:T:C	F215L	0.999
2:14634624:C:A	F215L	0.999
2:14634624:C:G	F215L	0.999
2:14634626:C:A	A216D	0.999
2:14634629:C:A	A217D	0.999
2:14634631:T:A	W218R	0.999
2:14634631:T:C	W218R	0.999

dbSNP variants (sampled 300 via entrez): RS1000211790 (2:14647940 A>G), RS1000215319 (2:14639235 C>T), RS1000305008 (2:14648350 C>T), RS1000307819 (2:14632573 G>A), RS1000383205 (2:14632771 G>T), RS1000501995 (2:14640880 G>A,C), RS1000641760 (2:14633725 G>A), RS1000641804 (2:14631184 T>C), RS1000715067 (2:14631559 A>G), RS1000911091 (2:14651042 T>C,G), RS1001014885 (2:14644242 A>T), RS1001068822 (2:14644473 T>C), RS1001357232 (2:14646588 T>A), RS1001368132 (2:14651315 T>C), RS1001369323 (2:14638980 A>G)

Disease associations

OMIM: gene MIM:611234 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST001523_2	Visceral adipose tissue adjusted for BMI	7.000000e-06
GCST002875_35	Diisocyanate-induced asthma	1.000000e-06
GCST002875_56	Diisocyanate-induced asthma	7.000000e-06
GCST002945_27	Emphysema imaging phenotypes	4.000000e-07
GCST008504_5	Fasting glucose change (long-term)	2.000000e-06
GCST011516_8	joint destruction in rheumatoid arthritis (rapid vs slow)	8.000000e-06
GCST011516_9	joint destruction in rheumatoid arthritis (rapid vs slow)	8.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0006995	response to diisocyanate
EFO:0007626	emphysema imaging measurement
EFO:0005413	joint damage measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression	4
entinostat	decreases expression, affects cotreatment	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Estradiol	affects cotreatment, decreases expression	2
Silicon Dioxide	increases expression	2
bisphenol F	affects cotreatment, decreases methylation	1
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, decreases expression	1
trichostatin A	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
zinc chromate	increases expression, increases abundance	1
ochratoxin A	decreases expression	1
chromium hexavalent ion	increases expression, increases abundance	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
NSC 689534	affects binding, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Calcitriol	increases expression	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	increases expression	1
Fluorouracil	increases expression	1
Gold	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Phenylmercuric Acetate	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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