LRRC24

Summary

LRRC24 (leucine rich repeat containing 24, HGNC:28947) is a protein-coding gene on chromosome 8q24.3, encoding Leucine-rich repeat-containing protein 24 (Q50LG9).

Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in external side of plasma membrane; extracellular matrix; and extracellular space.

Source: NCBI Gene 441381 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• MANE Select transcript: NM_001024678

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28947
Approved symbol	LRRC24
Name	leucine rich repeat containing 24
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	LRRC14OS
Ensembl gene	ENSG00000254402
Ensembl biotype	protein_coding
OMIM	620672
Entrez	441381

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000529415, ENST00000533758

RefSeq mRNA: 1 — MANE Select: NM_001024678 NM_001024678

CCDS: CCDS34969

Canonical transcript exons

ENST00000529415 — 5 exons

Exon	Start	End
ENSE00002146930	144526960	144527033
ENSE00002173439	144522388	144523409
ENSE00002329789	144524816	144525033
ENSE00002334047	144524110	144524278
ENSE00002356118	144524441	144524719

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 83.42.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2887 / max 39.0481, expressed in 494 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
95695	1.2887	494

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	83.42	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.84	silver quality
pituitary gland	UBERON:0000007	78.00	gold quality
adenohypophysis	UBERON:0002196	77.27	gold quality
hypothalamus	UBERON:0001898	77.21	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.11	gold quality
anterior cingulate cortex	UBERON:0009835	77.09	gold quality
superior frontal gyrus	UBERON:0002661	76.92	gold quality
lower esophagus mucosa	UBERON:0035834	76.75	gold quality
prefrontal cortex	UBERON:0000451	76.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	76.32	gold quality
frontal cortex	UBERON:0001870	75.94	gold quality
cerebral cortex	UBERON:0000956	75.68	gold quality
nucleus accumbens	UBERON:0001882	75.48	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.40	gold quality
right frontal lobe	UBERON:0002810	75.37	gold quality
brain	UBERON:0000955	74.48	gold quality
ganglionic eminence	UBERON:0004023	74.20	gold quality
primary visual cortex	UBERON:0002436	73.90	gold quality
cerebellar cortex	UBERON:0002129	73.60	gold quality
cerebellum	UBERON:0002037	73.58	gold quality
cerebellar hemisphere	UBERON:0002245	73.57	gold quality
temporal lobe	UBERON:0001871	73.30	gold quality
amygdala	UBERON:0001876	73.12	gold quality
substantia nigra	UBERON:0002038	72.88	gold quality
Ammon’s horn	UBERON:0001954	72.81	gold quality
ventricular zone	UBERON:0003053	72.63	gold quality
putamen	UBERON:0001874	72.51	gold quality
caudate nucleus	UBERON:0001873	72.22	gold quality
tibial nerve	UBERON:0001323	72.08	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.43

Regulation

Is transcription factor: no

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc24	ENSDARG00000101704
mus_musculus	Lrrc24	ENSMUSG00000033707
rattus_norvegicus	Lrrc24	ENSRNOG00000016204
drosophila_melanogaster	Con	FBGN0005775
drosophila_melanogaster	kek3	FBGN0028370
caenorhabditis_elegans	lron-9	WBGENE00011971
caenorhabditis_elegans		WBGENE00020649

Paralogs (22): CHADL (ENSG00000100399), LGI1 (ENSG00000108231), LGR6 (ENSG00000133067), CHAD (ENSG00000136457), LRIG3 (ENSG00000139263), LGR5 (ENSG00000139292), LRIG1 (ENSG00000144749), LRRTM2 (ENSG00000146006), LRIT1 (ENSG00000148602), LGI2 (ENSG00000153012), LGI4 (ENSG00000153902), LRRC52 (ENSG00000162763), ELFN2 (ENSG00000166897), LGI3 (ENSG00000168481), LRG1 (ENSG00000171236), CPN2 (ENSG00000178772), LRIT3 (ENSG00000183423), LRRC26 (ENSG00000184709), LRIG2 (ENSG00000198799), LGR4 (ENSG00000205213), ELFN1 (ENSG00000225968), TRIL (ENSG00000255690)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 24 — Q50LG9 (reviewed: Q50LG9)

All UniProt accessions (2): Q50LG9, G3V1D8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001019849* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000372	LRRNT	Domain
IPR000483	Cys-rich_flank_reg_C	Domain
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050333	SLRP	Family

Pfam: PF13855, PF13927

UniProt features (17 total): repeat 6, domain 3, glycosylation site 2, signal peptide 1, chain 1, region of interest 1, disulfide bond 1, sequence conflict 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q50LG9-F1	77.57	0.55

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 281–345

Glycosylation sites (2): 334, 363

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): GOBP_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOCC_CELL_SURFACE, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_SYNAPSE_STRUCTURE_OR_ACTIVITY, GOBP_CELL_JUNCTION_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS

GO Biological Process (1): positive regulation of synapse assembly (GO:0051965)

GO Molecular Function (2): signaling receptor activity (GO:0038023), protein binding (GO:0005515)

GO Cellular Component (3): plasma membrane (GO:0005886), external side of plasma membrane (GO:0009897), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
synapse assembly	1
positive regulation of nervous system development	1
regulation of synapse assembly	1
positive regulation of cell junction assembly	1
molecular transducer activity	1
binding	1
membrane	1
cell periphery	1
plasma membrane	1
cell surface	1
side of membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

738 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC24	LRRC14	Q15048	645
LRRC24	TLDC2	A0PJX2	549
LRRC24	SLC33A2	Q96ES6	541
LRRC24	GLI4	P10075	533
LRRC24	TMEM276	P0DTL5	510
LRRC24	DAD1	P46966	479
LRRC24	WDR97	A6NE52	479
LRRC24	PPP1R16A	Q96I34	475
LRRC24	ZNF837	Q96EG3	469
LRRC24	S4R3N1	S4R3N1	449
LRRC24	C1orf35	Q9BU76	446
LRRC24	ADCK5	Q3MIX3	443
LRRC24	DZANK1	Q9NVP4	417
LRRC24	APC2	O95996	417
LRRC24	TMEM131	Q92545	405
LRRC24	KIFC2	Q96AC6	405

IntAct

15 interactions, top by confidence:

A	B	Type	Score
GAA	B3GAT3	psi-mi:“MI:0914”(association)	0.530
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
CRP	QSOX1	psi-mi:“MI:0914”(association)	0.530
HLA-E	RTL8C	psi-mi:“MI:0914”(association)	0.350
HTR3B	TMEM223	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CCL3	KRBA1	psi-mi:“MI:0914”(association)	0.350
SCGB2A2	RTL8C	psi-mi:“MI:0914”(association)	0.350
C1orf54	AGRN	psi-mi:“MI:0914”(association)	0.350
GAA	ENTPD6	psi-mi:“MI:0914”(association)	0.350
MAN1A1	GPC4	psi-mi:“MI:0914”(association)	0.350
SFTPC	TMEM131L	psi-mi:“MI:0914”(association)	0.350
CEACAM21	GAPDHS	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-MS), LRRC24 (Affinity Capture-RNA)

ESM2 similar proteins: A1A4H9, A2ARI4, A2VDH3, A6H793, D4A6D8, E9Q7T7, F1MLX5, F1MT22, O75325, P59034, P59035, Q13641, Q149C3, Q3URE9, Q3UVD5, Q3UY51, Q4KLL3, Q4R8Y9, Q50LG9, Q5M8M9, Q5PQV5, Q5R6B1, Q5RDJ4, Q5VT99, Q6GQU6, Q6UY18, Q6ZSA7, Q7M6Z0, Q7TQ62, Q80WD1, Q86UE6, Q86UN2, Q86UN3, Q86WK6, Q8BHA1, Q8K0S5, Q8K377, Q8N7C0, Q91ZV8, Q96FE5

Diamond homologs: A3KNN3, A4IIW9, A6H789, A6H793, A6NJW4, A8WHP9, C3YZ59, E5DHB5, G5EFX6, O02678, O14498, O35367, O42235, O46542, O60938, O62702, O75093, O75094, O88186, O88279, O88280, O94813, P02750, P07585, P14770, P21793, P24014, P28654, P28675, P35379, P59034, P59035, P70193, P79763, Q01129, Q28888, Q29393, Q3SXY7, Q3UY51, Q3ZBN5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

796 predictions. Top by Δscore:

Variant	Effect	Δscore
8:144523406:TTCT:T	acceptor_gain	1.0000
8:144523408:CT:C	acceptor_gain	1.0000
8:144523410:C:CC	acceptor_gain	1.0000
8:144524105:GGTA:G	donor_loss	1.0000
8:144524106:GTAC:G	donor_loss	1.0000
8:144524107:TACCT:T	donor_loss	1.0000
8:144524108:A:T	donor_loss	1.0000
8:144524109:C:CA	donor_loss	1.0000
8:144524275:GTCG:G	acceptor_gain	1.0000
8:144524276:TCG:T	acceptor_gain	1.0000
8:144524277:CG:C	acceptor_gain	1.0000
8:144524277:CGC:C	acceptor_gain	1.0000
8:144524279:C:CC	acceptor_gain	1.0000
8:144524299:CG:C	acceptor_gain	1.0000
8:144524300:G:C	acceptor_gain	1.0000
8:144524435:GCTCA:G	donor_loss	1.0000
8:144524436:CTCA:C	donor_loss	1.0000
8:144524437:TCA:T	donor_loss	1.0000
8:144524438:CAC:C	donor_loss	1.0000
8:144524439:A:AC	donor_gain	1.0000
8:144524440:C:CC	donor_gain	1.0000
8:144524440:CCGG:C	donor_gain	1.0000
8:144523405:GTTCT:G	acceptor_gain	0.9900
8:144523409:TCTG:T	acceptor_loss	0.9900
8:144523410:C:CA	acceptor_loss	0.9900
8:144524274:AGTCG:A	acceptor_gain	0.9900
8:144524284:G:C	acceptor_gain	0.9900
8:144524284:G:GC	acceptor_gain	0.9900
8:144524294:C:CT	acceptor_gain	0.9900
8:144524300:G:GC	acceptor_gain	0.9900

AlphaMissense

3227 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:144522989:T:C	Y343C	0.999
8:144523138:C:A	W293C	0.999
8:144523138:C:G	W293C	0.999
8:144522983:C:G	C345S	0.998
8:144522984:A:T	C345S	0.998
8:144523401:A:G	W206R	0.998
8:144523401:A:T	W206R	0.998
8:144522984:A:G	C345R	0.997
8:144523140:A:G	W293R	0.997
8:144523140:A:T	W293R	0.997
8:144523175:C:G	C281S	0.997
8:144523176:A:G	C281R	0.997
8:144523176:A:T	C281S	0.997
8:144523246:G:C	C257W	0.997
8:144523247:C:G	C257S	0.997
8:144523247:C:T	C257Y	0.997
8:144523248:A:G	C257R	0.997
8:144523248:A:T	C257S	0.997
8:144523310:C:G	C236S	0.997
8:144523311:A:T	C236S	0.997
8:144524187:A:G	L177P	0.997
8:144522970:G:C	N349K	0.996
8:144522970:G:T	N349K	0.996
8:144522989:T:G	Y343S	0.996
8:144522990:A:C	Y343D	0.996
8:144523163:C:T	G285D	0.996
8:144523175:C:T	C281Y	0.996
8:144523394:C:G	C208S	0.996
8:144523395:A:T	C208S	0.996
8:144523399:C:A	W206C	0.996

dbSNP variants (sampled 300 via entrez): RS1000169767 (8:144525649 T>C), RS1000361671 (8:144522878 G>A,T), RS1000833019 (8:144528213 G>A,C), RS1002030586 (8:144524015 C>G,T), RS1002308949 (8:144528972 A>C), RS1003418907 (8:144528862 C>A), RS1003638690 (8:144529012 G>C,T), RS1003751900 (8:144525104 C>A,T), RS1003796114 (8:144524697 T>A), RS1004094189 (8:144527312 C>G,T), RS1004209036 (8:144524897 G>A), RS1004592665 (8:144523048 G>A), RS1004647605 (8:144522487 C>G), RS1004876247 (8:144526892 G>A), RS1006086444 (8:144525375 G>A)

Disease associations

OMIM: gene MIM:620672 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002598_30	Educational attainment	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004784	self reported educational attainment

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
Sunitinib	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	decreases expression	1
Smoke	decreases expression	1
Urethane	decreases expression, increases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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