LRRC43

Summary

LRRC43 (leucine rich repeat containing 43, HGNC:28562) is a protein-coding gene on chromosome 12q24.31, encoding Leucine-rich repeat-containing protein 43 (Q8N309).

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_001098519

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28562
Approved symbol	LRRC43
Name	leucine rich repeat containing 43
Location	12q24.31
Locus type	gene with protein product
Status	Approved
Aliases	MGC35140
Ensembl gene	ENSG00000158113
Ensembl biotype	protein_coding
Entrez	254050

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000339777, ENST00000537113, ENST00000537729, ENST00000537733, ENST00000538800, ENST00000541498, ENST00000907479

RefSeq mRNA: 2 — MANE Select: NM_001098519 NM_001098519, NM_152759

CCDS: CCDS45001

Canonical transcript exons

ENST00000339777 — 12 exons

Exon	Start	End
ENSE00001112137	122200189	122200330
ENSE00001112138	122191380	122191567
ENSE00001112139	122192745	122193004
ENSE00001382431	122190130	122190368
ENSE00002236939	122203315	122203471
ENSE00002254351	122183123	122183294
ENSE00003458747	122201296	122201329
ENSE00003543181	122200532	122200660
ENSE00003575611	122200746	122200934
ENSE00003639223	122184519	122184779
ENSE00003642927	122187701	122187840
ENSE00003654120	122186190	122186300

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 97.57.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5069 / max 13.9836, expressed in 286 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128512	0.5069	286

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.57	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.48	gold quality
ventral tegmental area	UBERON:0002691	85.77	gold quality
lateral globus pallidus	UBERON:0002476	85.15	gold quality
vena cava	UBERON:0004087	84.44	gold quality
cardia of stomach	UBERON:0001162	84.12	gold quality
sperm	CL:0000019	84.04	gold quality
inferior vagus X ganglion	UBERON:0005363	83.78	gold quality
thymus	UBERON:0002370	83.42	silver quality
penis	UBERON:0000989	83.34	silver quality
dorsal root ganglion	UBERON:0000044	83.27	gold quality
pharyngeal mucosa	UBERON:0000355	83.23	gold quality
nipple	UBERON:0002030	83.22	gold quality
substantia nigra pars reticulata	UBERON:0001966	82.94	gold quality
cerebellar vermis	UBERON:0004720	82.80	gold quality
lateral nuclear group of thalamus	UBERON:0002736	82.46	gold quality
substantia nigra pars compacta	UBERON:0001965	81.93	gold quality
trigeminal ganglion	UBERON:0001675	81.86	gold quality
medulla oblongata	UBERON:0001896	81.30	gold quality
pylorus	UBERON:0001166	80.98	gold quality
renal medulla	UBERON:0000362	80.90	gold quality
tongue	UBERON:0001723	80.81	gold quality
superior surface of tongue	UBERON:0007371	80.80	gold quality
body of tongue	UBERON:0011876	80.70	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.67	gold quality
superior vestibular nucleus	UBERON:0007227	80.55	gold quality
trachea	UBERON:0003126	80.49	gold quality
synovial joint	UBERON:0002217	80.31	gold quality
layer of synovial tissue	UBERON:0007616	80.26	gold quality
saphenous vein	UBERON:0007318	79.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.25

Regulation

Is transcription factor: no

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrrc43	ENSMUSG00000063409
rattus_norvegicus	Lrrc43	ENSRNOG00000008470
drosophila_melanogaster	TbCMF46	FBGN0032163
drosophila_melanogaster	Ppr-Y	FBGN0046697

Paralogs (13): LRRC23 (ENSG00000010626), LRRC61 (ENSG00000127399), DNAAF11 (ENSG00000129295), LRRC9 (ENSG00000131951), LRRCC1 (ENSG00000133739), LRRC49 (ENSG00000137821), LRRC46 (ENSG00000141294), DNAAF1 (ENSG00000154099), LRGUK (ENSG00000155530), LRRIQ3 (ENSG00000162620), DRC3 (ENSG00000171962), PPP1R42 (ENSG00000178125), CEP97 (ENSG00000182504)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 43 — Q8N309 (reviewed: Q8N309)

All UniProt accessions (2): Q8N309, F5H0N3

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N309-1	1	yes
Q8N309-2	2
Q8N309-3	3

RefSeq proteins (2): NP_001091989, NP_689972 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050576	Cilia_flagella_integrity	Family

Pfam: PF13855

UniProt features (14 total): repeat 4, splice variant 2, sequence variant 2, region of interest 2, compositionally biased region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N309-F1	74.90	0.54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): chr12q24, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, CBX7_TARGET_GENES, FOXN3_TARGET_GENES, SRPK2_TARGET_GENES, ZNF92_TARGET_GENES, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_EYE_MICROGLIA, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, GSE13887_ACT_CD4_VS_NO_TREATED_CD4_TCELL_UP, GSE3920_UNTREATED_VS_IFNG_TREATED_FIBROBLAST_UP, GSE32901_TH1_VS_TH17_ENRICHED_CD4_TCELL_UP

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

677 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC43	SPMIP10	Q6ZNM6	689
LRRC43	FAM181A	Q8N9Y4	601
LRRC43	CFAP141	Q5VU69	582
LRRC43	CFAP47	Q6ZTR5	566
LRRC43	ANKRD60	Q9BZ19	545
LRRC43	DYDC1	Q8WWB3	517
LRRC43	IQCK	Q8N0W5	488
LRRC43	CEP68	Q76N32	447
LRRC43	LRRC4	Q9HBW1	424
LRRC43	DCAF4	Q8WV16	419
LRRC43	SBF1	O95248	418
LRRC43	DCBLD2	Q96PD2	417
LRRC43	ENPP5	Q9UJA9	325
LRRC43	FILIP1	Q7Z7B0	323
LRRC43	PDZD2	O15018	310

IntAct

0 interactions, top by confidence:

BioGRID (2): DDX21 (Cross-Linking-MS (XL-MS)), LRRC43 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A6NFN9, B9EKE5, D3YYM4, D5K8A9, M0RAU5, O15259, P15943, P97432, Q08CH6, Q0IHI3, Q12789, Q14596, Q3MJ13, Q3V0L5, Q4R5A4, Q4R683, Q4R796, Q501R9, Q5F479, Q5M9F0, Q5RAX4, Q5RC14, Q5RC94, Q5RFQ4, Q5W0A0, Q5XX13, Q63505, Q6TDU7, Q76CY8, Q7L0X2, Q7TNH6, Q7Z7H3, Q86X53, Q8BHR8, Q8BMD5, Q8C0W1, Q8C761, Q8K284, Q8N309, Q8NDB2

Diamond homologs: Q3V0L5, Q8N309, Q95JT3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	81
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3201 predictions. Top by Δscore:

Variant	Effect	Δscore
12:122172737:TCCAC:T	acceptor_gain	1.0000
12:122172738:CCAC:C	acceptor_gain	1.0000
12:122172738:CCACC:C	acceptor_gain	1.0000
12:122172739:CAC:C	acceptor_gain	1.0000
12:122172739:CACC:C	acceptor_gain	1.0000
12:122172740:AC:A	acceptor_gain	1.0000
12:122172741:CC:C	acceptor_gain	1.0000
12:122172742:C:CA	acceptor_loss	1.0000
12:122172742:C:CC	acceptor_gain	1.0000
12:122172744:G:C	acceptor_gain	1.0000
12:122172744:G:GC	acceptor_gain	1.0000
12:122173840:TCAC:T	donor_loss	1.0000
12:122173841:CAC:C	donor_loss	1.0000
12:122173842:A:AC	donor_gain	1.0000
12:122173842:ACAT:A	donor_gain	1.0000
12:122173843:C:CA	donor_gain	1.0000
12:122173843:CA:C	donor_gain	1.0000
12:122173843:CAT:C	donor_gain	1.0000
12:122173843:CATC:C	donor_gain	1.0000
12:122173843:CATCT:C	donor_gain	1.0000
12:122174092:T:TA	donor_gain	1.0000
12:122174102:T:TA	donor_gain	1.0000
12:122183252:G:GT	donor_gain	1.0000
12:122183256:C:G	donor_gain	1.0000
12:122183291:C:G	donor_gain	1.0000
12:122184518:GA:G	acceptor_gain	1.0000
12:122184546:T:A	acceptor_gain	1.0000
12:122184776:GAAG:G	donor_gain	1.0000
12:122184777:AAG:A	donor_loss	1.0000
12:122184779:GG:G	donor_loss	1.0000

AlphaMissense

4221 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:122183271:T:C	F43L	0.993
12:122183273:C:A	F43L	0.993
12:122183273:C:G	F43L	0.993
12:122190147:T:C	L227P	0.990
12:122190308:G:C	D281H	0.989
12:122186239:T:C	L154S	0.988
12:122190241:C:A	N258K	0.987
12:122190241:C:G	N258K	0.987
12:122190309:A:T	D281V	0.985
12:122186296:T:A	L173H	0.984
12:122187711:T:C	L178P	0.984
12:122187721:T:A	N181K	0.984
12:122187721:T:G	N181K	0.984
12:122186260:T:C	I161T	0.983
12:122190163:C:A	N232K	0.983
12:122190163:C:G	N232K	0.983
12:122187705:T:C	L176P	0.982
12:122190306:T:C	L280P	0.982
12:122186255:T:A	N159K	0.981
12:122186255:T:G	N159K	0.981
12:122191503:T:A	V342E	0.981
12:122191508:T:G	Y344D	0.981
12:122183272:T:G	F43C	0.980
12:122187711:T:A	L178H	0.980
12:122190153:T:C	L229P	0.980
12:122186245:T:A	L156Q	0.979
12:122187777:T:C	L200S	0.979
12:122190143:T:C	S226P	0.979
12:122200293:T:C	L485P	0.979
12:122200285:G:C	K482N	0.978

dbSNP variants (sampled 300 via entrez): RS1000057433 (12:122183899 C>A,T), RS1000217729 (12:122199126 C>T), RS1000342979 (12:122203752 C>A,T), RS1000425697 (12:122200103 C>T), RS1000501121 (12:122200111 C>A,T), RS1000630846 (12:122168696 C>T), RS1000661876 (12:122169100 T>A,G), RS1000670876 (12:122192385 C>T), RS1000761608 (12:122198710 A>C,G), RS1000805950 (12:122189611 G>A,T), RS1000992958 (12:122203941 C>G,T), RS1001038535 (12:122193840 G>A), RS1001047474 (12:122189338 C>G,T), RS1001152661 (12:122170396 C>T), RS1001167798 (12:122197626 G>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST002740_77	Inflammatory skin disease	1.000000e-07
GCST005830_133	Hand grip strength	1.000000e-09
GCST007732_24	Allergic disease (asthma, hay fever or eczema)	3.000000e-08
GCST008163_107	Height	7.000000e-06
GCST012227_558	Hip circumference adjusted for BMI	2.000000e-08
GCST90020025_106	Waist-to-hip ratio adjusted for BMI	6.000000e-09
GCST90020025_112	Waist-to-hip ratio adjusted for BMI	1.000000e-08
GCST90020025_113	Waist-to-hip ratio adjusted for BMI	1.000000e-10
GCST90020026_28	Hip index	3.000000e-08
GCST90020027_1190	Waist-hip index	3.000000e-08
GCST90020027_1191	Waist-hip index	7.000000e-10
GCST90020027_1684	Waist-hip index	1.000000e-08
GCST90020028_955	Hip circumference adjusted for BMI	2.000000e-12
GCST90020028_960	Hip circumference adjusted for BMI	3.000000e-08
GCST90020028_961	Hip circumference adjusted for BMI	1.000000e-15
GCST90020028_963	Hip circumference adjusted for BMI	8.000000e-10
GCST90020029_467	Waist circumference adjusted for body mass index	3.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0006941	grip strength measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	affects methylation, increases methylation	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	increases reaction, affects binding	1
licochalcone B	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1
Lead	increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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