LRRC42

Summary

LRRC42 (leucine rich repeat containing 42, HGNC:28792) is a protein-coding gene on chromosome 1p32.3, encoding Leucine-rich repeat-containing protein 42 (Q9Y546).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_001256409

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28792
Approved symbol	LRRC42
Name	leucine rich repeat containing 42
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC8974
Ensembl gene	ENSG00000116212
Ensembl biotype	protein_coding
OMIM	620896
Entrez	115353

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 20 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000319223, ENST00000371368, ENST00000371370, ENST00000444987, ENST00000477905, ENST00000713564, ENST00000900033, ENST00000900034, ENST00000900035, ENST00000900036, ENST00000900037, ENST00000900038, ENST00000925869, ENST00000925870, ENST00000925871, ENST00000925872, ENST00000925873, ENST00000965713, ENST00000965714, ENST00000965715, ENST00000965716

RefSeq mRNA: 2 — MANE Select: NM_001256409 NM_001256409, NM_052940

CCDS: CCDS585

Canonical transcript exons

ENST00000371370 — 9 exons

Exon	Start	End
ENSE00000772726	53962296	53962409
ENSE00000772728	53962034	53962122
ENSE00000772729	53960356	53960474
ENSE00000772730	53958149	53958280
ENSE00000772731	53951986	53952472
ENSE00001399532	53947788	53947821
ENSE00003581592	53966296	53966380
ENSE00004020330	53967665	53968168
ENSE00004020331	53946350	53946549

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 94.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5924 / max 112.8107, expressed in 1802 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2933	11.4586	1781
2934	6.8450	1647
2932	2.2166	857
2935	0.0599	8
2936	0.0123	2

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	94.86	gold quality
secondary oocyte	CL:0000655	94.08	gold quality
islet of Langerhans	UBERON:0000006	93.51	gold quality
ventricular zone	UBERON:0003053	93.18	gold quality
ganglionic eminence	UBERON:0004023	92.37	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.04	gold quality
right adrenal gland	UBERON:0001233	91.32	gold quality
right adrenal gland cortex	UBERON:0035827	91.27	gold quality
left adrenal gland	UBERON:0001234	90.67	gold quality
left adrenal gland cortex	UBERON:0035825	90.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.31	gold quality
stromal cell of endometrium	CL:0002255	89.24	gold quality
adenohypophysis	UBERON:0002196	89.10	gold quality
adrenal gland	UBERON:0002369	88.91	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.81	gold quality
adrenal cortex	UBERON:0001235	88.49	gold quality
embryo	UBERON:0000922	88.15	gold quality
mucosa of stomach	UBERON:0001199	88.03	gold quality
pituitary gland	UBERON:0000007	87.88	gold quality
descending thoracic aorta	UBERON:0002345	87.76	gold quality
left lobe of thyroid gland	UBERON:0001120	87.74	gold quality
cortical plate	UBERON:0005343	87.68	gold quality
lower esophagus muscularis layer	UBERON:0035833	87.63	gold quality
lower esophagus	UBERON:0013473	87.62	gold quality
right lobe of thyroid gland	UBERON:0001119	87.57	gold quality
tibial nerve	UBERON:0001323	87.45	gold quality
skin of abdomen	UBERON:0001416	87.12	gold quality
skin of leg	UBERON:0001511	87.10	gold quality
esophagus	UBERON:0001043	86.99	gold quality
esophagus mucosa	UBERON:0002469	86.79	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.49

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting LRRC42, 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-3924	100.00	72.09	2394
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-944	99.82	70.85	3042

Literature-anchored findings (GeneRIF, showing 1)

• Findings suggest that LRRC42 overexpression as well as its interaction with LRRC42-GATAD2B might play essential roles in lung carcinogenesis. (PMID:24806090)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc42	ENSDARG00000030591
mus_musculus	Lrrc42	ENSMUSG00000028617
rattus_norvegicus	Lrrc42	ENSRNOG00000009983

Protein

Protein identifiers

Leucine-rich repeat-containing protein 42 — Q9Y546 (reviewed: Q9Y546)

All UniProt accessions (3): A6NL66, E7EP35, Q9Y546

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the LRRC42 family.

RefSeq proteins (2): NP_001243338, NP_443172 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR039631	LRRC42	Family

Pfam: PF13516

UniProt features (12 total): repeat 5, sequence conflict 3, modified residue 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y546-F1	72.48	0.43

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 (2): 406, 407

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): TAATAAT_MIR126, TAL1ALPHAE47_01, PATIL_LIVER_CANCER, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, ACEVEDO_LIVER_CANCER_UP, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN, TAL1BETAITF2_01, RP58_01, BAKKER_FOXO3_TARGETS_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, P53_DN.V1_UP, HHEX_TARGET_GENES, UBN1_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

384 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC42	GPR137C	Q8N3F9	568
LRRC42	HSF2BP	O75031	528
LRRC42	TRARG1	Q8IXB3	526
LRRC42	PPP1R14D	Q9NXH3	519
LRRC42	PBDC1	Q9BVG4	497
LRRC42	MPLKIP	Q8TAP9	496
LRRC42	RFNG	Q9Y644	478
LRRC42	SYCE2	Q6PIF2	472
LRRC42	SPATA22	Q8NHS9	471
LRRC42	ZBTB21	Q9ULJ3	453
LRRC42	HAUS8	Q9BT25	421
LRRC42	SNAP47	Q5SQN1	418
LRRC42	BSDC1	Q9NW68	418
LRRC42	WASHC2A	Q641Q2	416
LRRC42	M1AP	Q8TC57	416
LRRC42	MYOZ2	Q9NPC6	416

IntAct

10 interactions, top by confidence:

A	B	Type	Score
KAT5	YEATS4	psi-mi:“MI:0914”(association)	0.530
LRRC42	CUL3	psi-mi:“MI:0914”(association)	0.530
LRRC42	VDAC2	psi-mi:“MI:0915”(physical association)	0.400
LRRC42	RPS27A	psi-mi:“MI:0915”(physical association)	0.400
NLRP12	LRRC42	psi-mi:“MI:0915”(physical association)	0.370
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
LRRC42	CUL3	psi-mi:“MI:0914”(association)	0.350
KAT5	YEATS4	psi-mi:“MI:0914”(association)	0.350
TUBB	VWA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (31): LRRC42 (Affinity Capture-RNA), LRRC42 (Affinity Capture-RNA), LRRC42 (Affinity Capture-RNA), LRRC42 (Affinity Capture-RNA), SUGT1 (Affinity Capture-MS), PLXDC2 (Affinity Capture-MS), AMBRA1 (Affinity Capture-MS), LRRC42 (Affinity Capture-MS), CUL3 (Affinity Capture-MS), LRRC42 (Affinity Capture-MS), PLXDC2 (Affinity Capture-MS), SUGT1 (Affinity Capture-MS), LRRC42 (Synthetic Lethality), LRRC42 (Proximity Label-MS), LRRC42 (Affinity Capture-MS)

ESM2 similar proteins: A2RRS8, A2VE78, A5WW08, A6NFN9, C0HAC0, D3YYM4, O14607, O17482, P79457, Q08AW4, Q0V9Y8, Q2HJ90, Q2KI79, Q2YDQ5, Q3MJ13, Q3V0L5, Q4KLV2, Q4KM95, Q562E2, Q5F479, Q5R6E1, Q5RFQ4, Q5SUS0, Q5XGI3, Q5XX13, Q6B4Z3, Q6GPJ8, Q6GQ34, Q6GQV7, Q6INS1, Q6IRU7, Q6P1H6, Q6ZPF3, Q7TP65, Q7ZVU1, Q8C0W1, Q8C2S5, Q8IVF5, Q8IW35, Q8IZM8

Diamond homologs: Q0V9Y8, Q2HJ90, Q4KLV2, Q4KM95, Q6P5J6, Q8R2U7, Q9Y546

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1334 predictions. Top by Δscore:

Variant	Effect	Δscore
1:53946548:AGG:A	donor_loss	1.0000
1:53946551:T:G	donor_loss	1.0000
1:53952436:G:GT	donor_gain	1.0000
1:53958276:TCTAG:T	donor_loss	1.0000
1:53958277:CTAG:C	donor_loss	1.0000
1:53958278:TAG:T	donor_loss	1.0000
1:53958281:GT:G	donor_loss	1.0000
1:53958282:T:A	donor_loss	1.0000
1:53960353:TA:T	acceptor_loss	1.0000
1:53960354:A:AG	acceptor_gain	1.0000
1:53960354:A:AT	acceptor_loss	1.0000
1:53960354:AGT:A	acceptor_gain	1.0000
1:53960355:G:GA	acceptor_gain	1.0000
1:53960355:GT:G	acceptor_gain	1.0000
1:53960355:GTG:G	acceptor_gain	1.0000
1:53960355:GTGT:G	acceptor_gain	1.0000
1:53960355:GTGTA:G	acceptor_gain	1.0000
1:53960442:GCCT:G	donor_gain	1.0000
1:53960470:ATCAT:A	donor_gain	1.0000
1:53960471:TCAT:T	donor_gain	1.0000
1:53960471:TCATG:T	donor_loss	1.0000
1:53960472:CAT:C	donor_gain	1.0000
1:53960473:AT:A	donor_gain	1.0000
1:53960474:TGT:T	donor_loss	1.0000
1:53960475:G:GG	donor_gain	1.0000
1:53960475:GTA:G	donor_loss	1.0000
1:53960476:TAAG:T	donor_loss	1.0000
1:53966295:GATC:G	acceptor_gain	1.0000
1:53966369:C:G	donor_gain	1.0000
1:53966381:G:GG	donor_gain	1.0000

AlphaMissense

2801 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:53960383:T:A	N211K	0.997
1:53960383:T:G	N211K	0.997
1:53962398:T:A	W306R	0.997
1:53962398:T:C	W306R	0.997
1:53960373:T:C	L208P	0.996
1:53960463:T:C	L238S	0.996
1:53962400:G:C	W306C	0.996
1:53962400:G:T	W306C	0.996
1:53952352:T:C	L118P	0.995
1:53952421:T:C	F141S	0.995
1:53966308:T:A	W314R	0.995
1:53966308:T:C	W314R	0.995
1:53952354:T:C	F119L	0.994
1:53952356:C:A	F119L	0.994
1:53952356:C:G	F119L	0.994
1:53952420:T:C	F141L	0.994
1:53952422:C:A	F141L	0.994
1:53952422:C:G	F141L	0.994
1:53958214:T:C	L180P	0.994
1:53960367:T:C	L206P	0.994
1:53960469:T:C	L240S	0.994
1:53962097:T:C	L263S	0.994
1:53952343:C:A	A115D	0.993
1:53952355:T:C	F119S	0.993
1:53967926:T:C	L425S	0.993
1:53952319:T:A	L107H	0.992
1:53952328:T:C	F110S	0.992
1:53952382:T:C	F128S	0.992
1:53958208:T:C	L178P	0.992
1:53958214:T:A	L180H	0.992

dbSNP variants (sampled 300 via entrez): RS1000200831 (1:53949909 C>G), RS1000234590 (1:53965946 T>C), RS1000264949 (1:53948375 T>G), RS1000493632 (1:53964923 G>A), RS1000499240 (1:53956673 A>G), RS1000568528 (1:53964687 C>T), RS1000844235 (1:53960404 G>A), RS1000856803 (1:53945920 G>A,C,T), RS1000871324 (1:53951497 T>C), RS1001143817 (1:53959133 C>G), RS1001309108 (1:53946182 G>A), RS1001326440 (1:53964446 A>G), RS1001535867 (1:53946657 G>A,T), RS1001551588 (1:53958389 T>C,G), RS1001563287 (1:53953587 C>T)

Disease associations

OMIM: gene MIM:620896 | 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
GCST012353_10	Serum metabolite concentrations in chronic kidney disease	1.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, affects cotreatment, increases expression	2
Cisplatin	affects expression, increases expression	2
Valproic Acid	affects expression, decreases methylation	2
afuresertib	decreases expression	1
TAK-243	increases sumoylation	1
beta-lapachone	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
monomethylarsonous acid	decreases expression	1
Decitabine	affects expression	1
Benzo(a)pyrene	affects methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	decreases expression, increases abundance	1
Methapyrilene	increases methylation	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases methylation	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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