LRRC58

Summary

LRRC58 (leucine rich repeat containing 58, HGNC:26968) is a protein-coding gene on chromosome 3q13.33, encoding Leucine-rich repeat-containing protein 58 (Q96CX6).

Predicted to be involved in intracellular signal transduction.

Source: NCBI Gene 116064 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_001099678

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26968
Approved symbol	LRRC58
Name	leucine rich repeat containing 58
Location	3q13.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000163428
Ensembl biotype	protein_coding
Entrez	116064

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000295628, ENST00000886041, ENST00000946153

RefSeq mRNA: 1 — MANE Select: NM_001099678 NM_001099678

CCDS: CCDS46892

Canonical transcript exons

ENST00000295628 — 4 exons

Exon	Start	End
ENSE00001074429	120334862	120335139
ENSE00001074433	120335825	120335953
ENSE00001074437	120348744	120349354
ENSE00001074440	120324509	120331408

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 97.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0833 / max 232.4783, expressed in 1794 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
44054	15.3489	1779
44053	1.6238	1033
44056	0.6978	430
44055	0.4128	193

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	97.12	gold quality
ileal mucosa	UBERON:0000331	95.54	gold quality
adrenal tissue	UBERON:0018303	94.52	gold quality
tibia	UBERON:0000979	93.72	gold quality
superficial temporal artery	UBERON:0001614	92.94	gold quality
mucosa of paranasal sinus	UBERON:0005030	92.88	gold quality
kidney epithelium	UBERON:0004819	92.83	gold quality
epithelial cell of pancreas	CL:0000083	92.63	silver quality
cauda epididymis	UBERON:0004360	92.53	gold quality
layer of synovial tissue	UBERON:0007616	92.30	gold quality
tibialis anterior	UBERON:0001385	92.09	gold quality
upper leg skin	UBERON:0004262	91.68	gold quality
pigmented layer of retina	UBERON:0001782	91.55	gold quality
retina	UBERON:0000966	91.53	gold quality
pancreatic ductal cell	CL:0002079	91.46	silver quality
skin of hip	UBERON:0001554	91.11	gold quality
ventricular zone	UBERON:0003053	90.63	gold quality
penis	UBERON:0000989	90.51	gold quality
eye	UBERON:0000970	90.41	gold quality
subthalamic nucleus	UBERON:0001906	90.41	gold quality
parietal pleura	UBERON:0002400	90.41	gold quality
synovial joint	UBERON:0002217	90.35	gold quality
medial globus pallidus	UBERON:0002477	90.33	gold quality
globus pallidus	UBERON:0001875	90.32	gold quality
palpebral conjunctiva	UBERON:0001812	90.05	gold quality
caput epididymis	UBERON:0004358	89.87	gold quality
corpus epididymis	UBERON:0004359	89.78	gold quality
oral cavity	UBERON:0000167	89.64	gold quality
mammalian vulva	UBERON:0000997	89.31	gold quality
epithelium of nasopharynx	UBERON:0001951	89.26	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-CURD-88	yes	43.81
E-GEOD-137537	yes	7.64
E-HCAD-10	yes	4.27
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

263 targeting LRRC58, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6888-3P	99.97	65.95	1170

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc58b	ENSDARG00000063509
danio_rerio	lrrc58a	ENSDARG00000076773
mus_musculus	Lrrc58	ENSMUSG00000034158
rattus_norvegicus	Lrrc58	ENSRNOG00000027151
drosophila_melanogaster	CG32687	FBGN0052687
caenorhabditis_elegans		WBGENE00021533

Paralogs (31): LRRC7 (ENSG00000033122), PHLPP2 (ENSG00000040199), LRRC40 (ENSG00000066557), LRCH4 (ENSG00000077454), PHLPP1 (ENSG00000081913), SHOC2 (ENSG00000108061), ERBIN (ENSG00000112851), LRRC39 (ENSG00000122477), LRCH2 (ENSG00000130224), LRCH1 (ENSG00000136141), LRRC8A (ENSG00000136802), LRRC1 (ENSG00000137269), MFHAS1 (ENSG00000147324), LRRC27 (ENSG00000148814), LRRK1 (ENSG00000154237), LRRC2 (ENSG00000163827), LRRC18 (ENSG00000165383), LRRC28 (ENSG00000168904), LRRC8E (ENSG00000171017), LRRC8C (ENSG00000171488), LRRC8D (ENSG00000171492), PIDD1 (ENSG00000177595), SCRIB (ENSG00000180900), LRCH3 (ENSG00000186001), LRRIQ4 (ENSG00000188306), LRRC8B (ENSG00000197147), LRRC10 (ENSG00000198812), LRRC10B (ENSG00000204950), LRRC30 (ENSG00000206422), LRRC69 (ENSG00000214954), LRRD1 (ENSG00000240720)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 58 — Q96CX6 (reviewed: Q96CX6)

All UniProt accessions (1): Q96CX6

RefSeq proteins (1): NP_001093148* (*=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
IPR050715	LRR-SigEffector_domain	Family

Pfam: PF00560, PF13855

UniProt features (13 total): repeat 9, chain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9T7V	ELECTRON MICROSCOPY	2.95

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96CX6-F1	77.61	0.49

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): 24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 149 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, WEI_MYCN_TARGETS_WITH_E_BOX, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, SENESE_HDAC1_TARGETS_UP, CHANDRAN_METASTASIS_UP, MARSON_BOUND_BY_FOXP3_STIMULATED, NUYTTEN_NIPP1_TARGETS_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, KAMIKUBO_MYELOID_MN1_NETWORK, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_12H_UP

GO Biological Process (1): intracellular signal transduction (GO:0035556)

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
intracellular anatomical structure	1
signal transduction	1
binding	1

Protein interactions and networks

STRING

774 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC58	ZNF860	A6NHJ4	541
LRRC58	GPR156	Q8NFN8	503
LRRC58	TOPAZ1	Q8N9V7	473
LRRC58	LRRC26	Q2I0M4	456
LRRC58	DZIP1L	Q8IYY4	446
LRRC58	LRRC52	Q8N7C0	439
LRRC58	GPR149	Q86SP6	422
LRRC58	LRRC3B	Q96PB8	417
LRRC58	BEND6	Q5SZJ8	416
LRRC58	CAND2	O75155	407
LRRC58	TMEM167A	Q8TBQ9	405
LRRC58	OSBPL10	Q9BXB5	375
LRRC58	TAFA4	Q96LR4	374
LRRC58	NUDT16	Q96DE0	370
LRRC58	CASKIN2	Q8WXE0	369
LRRC58	BORCS5	Q969J3	369

IntAct

10 interactions, top by confidence:

A	B	Type	Score
CUL5	SOCS7	psi-mi:“MI:0914”(association)	0.640
SKP2	DPYSL4	psi-mi:“MI:0914”(association)	0.530
CDO1	DBT	psi-mi:“MI:0914”(association)	0.530
ATG14	CETN2	psi-mi:“MI:0914”(association)	0.530
	LRRC58	psi-mi:“MI:0915”(physical association)	0.400
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ATG14	MAP4K4	psi-mi:“MI:0914”(association)	0.350

BioGRID (23): LRRC58 (Affinity Capture-RNA), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), LRRC58 (Affinity Capture-MS), TCEB2 (Affinity Capture-MS)

ESM2 similar proteins: A0JM56, A0JPI9, A4IHG1, A5PK13, D3YY91, F1ND48, O35125, Q13309, Q15813, Q24K06, Q32KP2, Q32KS0, Q32L08, Q32NT4, Q3KQF4, Q3KRC6, Q3UGP9, Q498T9, Q4U2V3, Q5BKY1, Q5DU41, Q5FVQ9, Q5PQJ7, Q5QJ74, Q5R8X9, Q5RBD9, Q5U378, Q66JT1, Q68F79, Q6GQN5, Q6NSJ5, Q6NU09, Q6P9F7, Q6WRX3, Q6ZNQ3, Q8C5W3, Q8CDN9, Q8CIV8, Q8IY45, Q8IZ02

Diamond homologs: A4IHG1, Q32NT4, Q3UGP9, Q6XHA6, Q96CX6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

612 predictions. Top by Δscore:

Variant	Effect	Δscore
3:120331356:C:A	donor_gain	1.0000
3:120334857:CTTA:C	donor_loss	1.0000
3:120334858:TTA:T	donor_loss	1.0000
3:120334859:TA:T	donor_loss	1.0000
3:120334860:ACCT:A	donor_gain	1.0000
3:120334861:CCT:C	donor_gain	1.0000
3:120334861:CCTC:C	donor_gain	1.0000
3:120335823:A:AC	donor_gain	1.0000
3:120335824:C:CT	donor_gain	1.0000
3:120348740:TCA:T	donor_loss	1.0000
3:120348741:CAC:C	donor_loss	1.0000
3:120348743:CCT:C	donor_gain	1.0000
3:120331217:T:A	donor_gain	0.9900
3:120331355:T:TA	donor_gain	0.9900
3:120334860:A:AC	donor_gain	0.9900
3:120334861:C:CG	donor_gain	0.9900
3:120335117:T:C	acceptor_gain	0.9900
3:120335137:AACC:A	acceptor_loss	0.9900
3:120335138:ACCT:A	acceptor_loss	0.9900
3:120335139:CCT:C	acceptor_loss	0.9900
3:120335140:C:A	acceptor_loss	0.9900
3:120335140:C:CC	acceptor_gain	0.9900
3:120335816:ACTAC:A	donor_loss	0.9900
3:120335817:CTACT:C	donor_loss	0.9900
3:120335818:TAC:T	donor_loss	0.9900
3:120335819:AC:A	donor_loss	0.9900
3:120335820:C:CA	donor_loss	0.9900
3:120335821:T:TA	donor_loss	0.9900
3:120335822:CACTG:C	donor_loss	0.9900
3:120335823:A:C	donor_loss	0.9900

AlphaMissense

2348 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:120334883:A:G	C296R	1.000
3:120335034:A:C	N245K	1.000
3:120335034:A:T	N245K	1.000
3:120331325:A:G	C331R	0.999
3:120331362:G:C	F318L	0.999
3:120331362:G:T	F318L	0.999
3:120331364:A:G	F318L	0.999
3:120331371:A:C	F315L	0.999
3:120331371:A:T	F315L	0.999
3:120331373:A:G	F315L	0.999
3:120334867:C:G	C301S	0.999
3:120334868:A:G	C301R	0.999
3:120334868:A:T	C301S	0.999
3:120334881:G:C	C296W	0.999
3:120334882:C:G	C296S	0.999
3:120334883:A:T	C296S	0.999
3:120334966:C:G	R268P	0.999
3:120335016:A:C	F251L	0.999
3:120335016:A:T	F251L	0.999
3:120335018:A:G	F251L	0.999
3:120335036:T:A	N245Y	0.999
3:120335036:T:C	N245D	0.999
3:120335044:A:G	L242S	0.999
3:120335046:A:C	S241R	0.999
3:120335046:A:T	S241R	0.999
3:120335048:T:G	S241R	0.999
3:120335050:A:G	L240S	0.999
3:120335059:A:C	L237W	0.999
3:120335103:G:C	N222K	0.999
3:120335103:G:T	N222K	0.999

dbSNP variants (sampled 300 via entrez): RS1000054844 (3:120345514 T>C), RS1000068428 (3:120330017 T>A,C), RS1000097103 (3:120325642 A>T), RS1000121522 (3:120345786 G>A,C), RS1000308175 (3:120332887 C>T), RS1000344971 (3:120331744 C>A), RS1000349056 (3:120348471 T>C), RS1000461703 (3:120348759 A>T), RS1000549807 (3:120326280 T>C), RS1000622636 (3:120336794 A>AT), RS1000634592 (3:120339083 G>A), RS1000643087 (3:120342827 C>A,T), RS1000735246 (3:120336474 A>C,G), RS1000877001 (3:120324568 A>G), RS1000898406 (3:120326592 A>G)

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

2 associations (top):

Study	Trait	p-value
GCST001353_9	HIV-1 susceptibility	8.000000e-06
GCST001514_12	Economic and political preferences (feminism/equality)	8.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0000180	HIV-1 infection
EFO:0004827	economic and social preference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression, decreases expression, affects cotreatment	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
Benzo(a)pyrene	increases expression, decreases expression	2
Cisplatin	affects expression, decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
geldanamycin	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases abundance, affects cotreatment, decreases expression	1
bisphenol A	increases expression	1
trichostatin A	increases expression	1
2-butenal	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline	increases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
dibenzo(a,l)pyrene	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
jinfukang	decreases expression	1
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Cadmium	increases abundance, increases expression	1
Calcitriol	increases expression	1
Estradiol	increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1W5	Abcam HeLa LRRC58 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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