LRRC20

Summary

LRRC20 (leucine rich repeat containing 20, HGNC:23421) is a protein-coding gene on chromosome 10q22.1, encoding Leucine-rich repeat-containing protein 20 (Q8TCA0).

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_001278212

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23421
Approved symbol	LRRC20
Name	leucine rich repeat containing 20
Location	10q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10751, FLJ10844
Ensembl gene	ENSG00000172731
Ensembl biotype	protein_coding
Entrez	55222

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 18 protein_coding

ENST00000355790, ENST00000357631, ENST00000358141, ENST00000373224, ENST00000395010, ENST00000395011, ENST00000446961, ENST00000890382, ENST00000890383, ENST00000890384, ENST00000931937, ENST00000958347, ENST00000958348, ENST00000958349, ENST00000958350, ENST00000958351, ENST00000958352, ENST00000958353

RefSeq mRNA: 7 — MANE Select: NM_001278212 NM_001278211, NM_001278212, NM_001278213, NM_001278214, NM_018205, NM_018239, NM_207119

CCDS: CCDS7300, CCDS7301, CCDS7302, CCDS73145

Canonical transcript exons

ENST00000446961 — 5 exons

Exon	Start	End
ENSE00001186071	70323863	70324030
ENSE00001186095	70376452	70376596
ENSE00001684043	70298975	70301508
ENSE00001742745	70382549	70382625
ENSE00003711493	70340553	70340702

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 97.70.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.4845 / max 51.3332, expressed in 1027 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109841	2.2054	1012
109836	0.1312	17
109837	0.0639	28
109839	0.0565	16
109835	0.0192	8
109840	0.0082	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
hindlimb stylopod muscle	UBERON:0004252	97.70	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.79	gold quality
gastrocnemius	UBERON:0001388	96.20	gold quality
triceps brachii	UBERON:0001509	95.49	gold quality
muscle of leg	UBERON:0001383	95.38	gold quality
muscle organ	UBERON:0001630	95.23	gold quality
vastus lateralis	UBERON:0001379	95.16	gold quality
skeletal muscle tissue	UBERON:0001134	95.03	gold quality
quadriceps femoris	UBERON:0001377	94.65	gold quality
apex of heart	UBERON:0002098	94.57	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.31	gold quality
diaphragm	UBERON:0001103	93.67	gold quality
gluteal muscle	UBERON:0002000	93.67	gold quality
biceps brachii	UBERON:0001507	93.55	gold quality
lower esophagus mucosa	UBERON:0035834	93.21	gold quality
muscle tissue	UBERON:0002385	92.26	gold quality
deltoid	UBERON:0001476	90.78	gold quality
heart left ventricle	UBERON:0002084	89.88	gold quality
cardiac ventricle	UBERON:0002082	89.54	gold quality
cortical plate	UBERON:0005343	89.27	gold quality
right frontal lobe	UBERON:0002810	89.21	gold quality
prefrontal cortex	UBERON:0000451	88.95	gold quality
body of tongue	UBERON:0011876	88.70	gold quality
anterior cingulate cortex	UBERON:0009835	87.68	gold quality
cingulate cortex	UBERON:0003027	87.66	gold quality
ganglionic eminence	UBERON:0004023	87.43	gold quality
right lobe of liver	UBERON:0001114	87.38	gold quality
frontal cortex	UBERON:0001870	87.04	gold quality
neocortex	UBERON:0001950	86.96	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.53	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6142	no	65.66
E-ANND-3	no	2.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

75 targeting LRRC20, 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-4283	100.00	66.42	2097
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4644	99.35	69.12	2514

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc20	ENSDARG00000105018
mus_musculus	Lrrc20	ENSMUSG00000037151
rattus_norvegicus	Lrrc20	ENSRNOG00000000560
drosophila_melanogaster	Sclp	FBGN0030357
caenorhabditis_elegans		WBGENE00010675

Protein

Protein identifiers

Leucine-rich repeat-containing protein 20 — Q8TCA0 (reviewed: Q8TCA0)

All UniProt accessions (3): A0A0A0MS58, Q8TCA0, X6RK58

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt ID	Names	Canonical?
Q8TCA0-1	1	yes
Q8TCA0-2	2
Q8TCA0-3	3

RefSeq proteins (7): NP_001265140, NP_001265141, NP_001265142, NP_001265143, NP_060675, NP_060709, NP_997002 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050216	LRR_domain-containing	Family

Pfam: PF13855

UniProt features (9 total): repeat 5, splice variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TCA0-F1	94.64	0.90

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): 175

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, MAZ_Q6, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, CCCNNGGGAR_OLF1_01, MEF2_Q6_01, CTAWWWATA_RSRFC4_Q2, SENESE_HDAC3_TARGETS_DN, NUYTTEN_EZH2_TARGETS_DN, MEF2_03, MULLIGHAN_MLL_SIGNATURE_1_UP, RORA2_01, MARTENS_BOUND_BY_PML_RARA_FUSION, PRC2_EED_DN.V1_DN, PRC2_EZH2_UP.V1_DN

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

768 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC20	LRRC30	A6NM36	568
LRRC20	LRRC14B	A6NHZ5	548
LRRC20	ASB12	Q8WXK4	523
LRRC20	PRR29	P0C7W0	507
LRRC20	ANKS1A	Q92625	492
LRRC20	PRRG2	O14669	491
LRRC20	PLEKHG4B	Q96PX9	477
LRRC20	LRRC38	Q5VT99	465
LRRC20	TMEM69	Q5SWH9	464
LRRC20	LRRC23	Q53EV4	462
LRRC20	ASB8	Q9H765	459
LRRC20	TMEM38A	Q9H6F2	450
LRRC20	CCDC71	Q8IV32	434
LRRC20	VSIG2	Q96IQ7	417
LRRC20	CCDC47	Q96A33	390

IntAct

27 interactions, top by confidence:

A	B	Type	Score
LRRC20	ZBED1	psi-mi:“MI:0915”(physical association)	0.720
ZBED1	LRRC20	psi-mi:“MI:0915”(physical association)	0.720
TOM1	LRRC20	psi-mi:“MI:0915”(physical association)	0.560
ACTBL2	POTEF	psi-mi:“MI:0914”(association)	0.530
LRRC20	ACTB	psi-mi:“MI:0914”(association)	0.530
LRRC20	PCNA	psi-mi:“MI:0915”(physical association)	0.370
ACTB	ENAH	psi-mi:“MI:0914”(association)	0.350
LRRC20	POTEI	psi-mi:“MI:0914”(association)	0.350
GPN1	A2ML1	psi-mi:“MI:0914”(association)	0.350
FOSL1	AHCYL1	psi-mi:“MI:0914”(association)	0.350
ACTBL2	BTN1A1	psi-mi:“MI:0914”(association)	0.350
DDX28	UBA6	psi-mi:“MI:0914”(association)	0.350
GAB2	UBA6	psi-mi:“MI:0914”(association)	0.350
IRF2BP1	KLHL12	psi-mi:“MI:0914”(association)	0.350
MARS2	DDX39A	psi-mi:“MI:0914”(association)	0.350
NPPB	ACOT7	psi-mi:“MI:0914”(association)	0.350
PEX7	UBA6	psi-mi:“MI:0914”(association)	0.350
RAE1	NHERF1	psi-mi:“MI:0914”(association)	0.350
VENTX	UBA6	psi-mi:“MI:0914”(association)	0.350
LRRC20	ZBED1	psi-mi:“MI:0915”(physical association)	0.000
LRRC20	TOM1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): LRRC20 (Two-hybrid), LRRC20 (Affinity Capture-MS), LRRC20 (Biochemical Activity), LRRC20 (Two-hybrid), ZBED1 (Two-hybrid), LRRC20 (Negative Genetic), ACTB (Affinity Capture-MS), POTEI (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), SUGT1 (Affinity Capture-MS), LRRC20 (Affinity Capture-MS), ACTC1 (Affinity Capture-MS), LRRC20 (Affinity Capture-MS), LRRC20 (Affinity Capture-MS)

ESM2 similar proteins: A0A096MJZ0, D0MYB4, O35125, O94489, P09661, P0C895, P11745, P22194, P36047, P41391, P43333, P45969, P57784, Q05A62, Q08963, Q15435, Q28G94, Q2KID4, Q32PL1, Q3T0W4, Q3UM45, Q4LDG9, Q4P5F9, Q4R8Y8, Q4V8D9, Q4WV66, Q54Q39, Q5BGW9, Q5FVQ9, Q5HZV9, Q5RFS7, Q5U378, Q5U508, Q641R9, Q6BT60, Q6C417, Q6DHB1, Q6DIQ3, Q6GPJ5, Q7S9P4

Diamond homologs: Q8CI70, Q8TCA0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1694 predictions. Top by Δscore:

Variant	Effect	Δscore
10:70301504:CACAT:C	acceptor_gain	1.0000
10:70301505:ACAT:A	acceptor_gain	1.0000
10:70301506:CAT:C	acceptor_gain	1.0000
10:70301506:CATC:C	acceptor_gain	1.0000
10:70301507:AT:A	acceptor_gain	1.0000
10:70301507:ATCT:A	acceptor_loss	1.0000
10:70301509:C:CC	acceptor_gain	1.0000
10:70301509:CT:C	acceptor_loss	1.0000
10:70301512:T:TC	acceptor_gain	1.0000
10:70323858:CTCA:C	donor_loss	1.0000
10:70323861:A:AC	donor_gain	1.0000
10:70323861:ACCT:A	donor_loss	1.0000
10:70323862:C:CC	donor_gain	1.0000
10:70323862:C:CG	donor_loss	1.0000
10:70323862:CCTA:C	donor_gain	1.0000
10:70323866:CGAT:C	donor_gain	1.0000
10:70324029:CT:C	acceptor_gain	1.0000
10:70324031:C:CC	acceptor_gain	1.0000
10:70324034:CCACG:C	acceptor_gain	1.0000
10:70324035:C:CT	acceptor_gain	1.0000
10:70324037:CG:C	acceptor_gain	1.0000
10:70324038:G:C	acceptor_gain	1.0000
10:70324038:G:GC	acceptor_gain	1.0000
10:70324041:C:CT	acceptor_gain	1.0000
10:70324042:A:T	acceptor_gain	1.0000
10:70340599:AAG:A	donor_gain	1.0000
10:70340599:AAGCT:A	donor_gain	1.0000
10:70340710:C:CT	acceptor_gain	1.0000
10:70340710:C:T	acceptor_gain	1.0000
10:70340711:A:T	acceptor_gain	1.0000

AlphaMissense

1139 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:70323873:G:C	N130K	0.996
10:70323873:G:T	N130K	0.996
10:70323874:T:A	N130I	0.996
10:70324011:G:C	N84K	0.996
10:70324011:G:T	N84K	0.996
10:70323883:A:G	L127P	0.995
10:70323952:A:G	L104P	0.995
10:70324027:A:G	L79P	0.995
10:70323875:T:A	N130Y	0.994
10:70323937:A:G	F109S	0.993
10:70323942:G:C	N107K	0.993
10:70323942:G:T	N107K	0.993
10:70324021:A:G	L81P	0.993
10:70340675:A:G	F37S	0.993
10:70324027:A:T	L79H	0.992
10:70340606:T:A	N60I	0.992
10:70323875:T:G	N130H	0.991
10:70323943:T:A	N107I	0.991
10:70323958:A:T	I102N	0.991
10:70323967:A:T	L99H	0.991
10:70340605:G:C	N60K	0.991
10:70340605:G:T	N60K	0.991
10:70340699:A:G	L29P	0.991
10:70323889:A:T	I125N	0.990
10:70323952:A:T	L104Q	0.990
10:70340615:A:G	L57P	0.990
10:70376454:A:G	L27P	0.990
10:70301447:G:C	N154K	0.989
10:70301447:G:T	N154K	0.989
10:70301457:A:G	L151P	0.989

dbSNP variants (sampled 300 via entrez): RS1000067477 (10:70345474 A>T), RS1000128580 (10:70372673 A>C), RS1000132474 (10:70369623 A>C), RS1000148166 (10:70304917 G>A), RS1000174158 (10:70334726 C>A), RS1000185373 (10:70369316 G>A,T), RS1000194015 (10:70328303 C>T), RS1000210838 (10:70352669 T>G), RS1000387126 (10:70316741 G>T), RS1000422598 (10:70357570 G>A,C), RS1000428531 (10:70317110 G>A), RS1000440921 (10:70362427 T>C), RS1000474891 (10:70357346 C>A,T), RS1000484747 (10:70322628 G>C), RS1000500598 (10:70304532 T>C)

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

3 associations (top):

Study	Trait	p-value
GCST001889_5	Brain connectivity	9.000000e-10
GCST003075_140	Cognitive decline rate in late mild cognitive impairment	3.000000e-07
GCST003075_7	Cognitive decline rate in late mild cognitive impairment	8.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007710	cognitive decline measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression, increases abundance	4
Arsenic	affects methylation, decreases expression, increases abundance	4
Benzo(a)pyrene	decreases expression, increases methylation	4
bisphenol A	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
sodium arsenate	decreases expression, increases abundance	1
trichostatin A	decreases expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects response to substance, increases expression, affects cotreatment	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	decreases 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	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	decreases expression, affects binding	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1

Clinical trials (associated diseases)

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