LRRC30

Summary

LRRC30 (leucine rich repeat containing 30, HGNC:30219) is a protein-coding gene on chromosome 18p11.23, encoding Leucine-rich repeat-containing protein 30 (A6NM36).

Predicted to be involved in intracellular signal transduction.

Source: NCBI Gene 339291 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_001105581

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30219
Approved symbol	LRRC30
Name	leucine rich repeat containing 30
Location	18p11.23
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000206422
Ensembl biotype	protein_coding
Entrez	339291

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000383467

RefSeq mRNA: 1 — MANE Select: NM_001105581 NM_001105581

CCDS: CCDS42409

Canonical transcript exons

ENST00000383467 — 1 exons

Exon	Start	End
ENSE00001497097	7231089	7232044

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 84.83.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skeletal muscle tissue	UBERON:0001134	84.83	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.66	gold quality
gastrocnemius	UBERON:0001388	77.10	gold quality
muscle of leg	UBERON:0001383	76.59	gold quality
muscle tissue	UBERON:0002385	68.89	gold quality
bone marrow cell	CL:0002092	38.47	gold quality
apex of heart	UBERON:0002098	38.15	silver quality
granulocyte	CL:0000094	37.52	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
sural nerve	UBERON:0015488	37.10	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
bone marrow	UBERON:0002371	32.92	gold quality
tonsil	UBERON:0002372	32.65	gold quality
leukocyte	CL:0000738	30.47	gold quality
monocyte	CL:0000576	30.11	gold quality
heart left ventricle	UBERON:0002084	29.90	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.32	gold quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	28.12	gold quality
lymph node	UBERON:0000029	27.57	gold quality
heart	UBERON:0000948	27.34	gold quality
blood	UBERON:0000178	27.15	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.98

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc30a	ENSDARG00000029710
mus_musculus	Lrrc30	ENSMUSG00000073375
rattus_norvegicus	Lrrc30	ENSRNOG00000030389
drosophila_melanogaster	f-cup	FBGN0028487
drosophila_melanogaster	CG3494	FBGN0035008

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), LRRC58 (ENSG00000163428), 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), LRRC69 (ENSG00000214954), LRRD1 (ENSG00000240720)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 30 — A6NM36 (reviewed: A6NM36)

All UniProt accessions (1): A6NM36

RefSeq proteins (1): NP_001099051* (*=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: PF00560, PF13855

UniProt features (11 total): repeat 9, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NM36-F1	90.03	0.80

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): GSE13522_WT_VS_IFNG_KO_SKIN_DN, GLI1_TARGET_GENES, SIX1_TARGET_GENES, GSE11884_WT_VS_FURIN_KO_NAIVE_CD4_TCELL_UP, ZAK_PBMC_MRKAD5_HIV_1_GAG_POL_NEF_AGE_20_50YO_CORRELATED_WITH_CD8_T_CELL_RESPONSE_3DY_NEGATIVE, GSE9946_MATURE_STIMULATORY_VS_LISTERIA_INF_MATURE_DC_DN, GSE11367_CTRL_VS_IL17_TREATED_SMOOTH_MUSCLE_CELL_UP, chr18p11, GSE37563_WT_VS_CTLA4_KO_CD4_TCELL_D4_POST_IMMUNIZATION_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

816 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC30	ESPNL	Q6ZVH7	573
LRRC30	LRRC14B	A6NHZ5	570
LRRC30	LRRC20	Q8TCA0	568
LRRC30	ANKRD12	Q6UB98	559
LRRC30	ASB12	Q8WXK4	539
LRRC30	CYP26C1	Q6V0L0	497
LRRC30	PTPRM	P28827	491
LRRC30	TWSG1	Q9GZX9	490
LRRC30	LRRC38	Q5VT99	488
LRRC30	NDUFV2	P19404	478
LRRC30	ASB8	Q9H765	463
LRRC30	ELF4	Q99607	458
LRRC30	PPP4R1	Q8TF05	449
LRRC30	TMEM38A	Q9H6F2	437
LRRC30	VWA2	Q5GFL6	430

IntAct

0 interactions, top by confidence:

BioGRID (1): LRRC30 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A4D1F6, A4IIK1, A6H6A4, A6NIV6, A6NM36, C0STK7, D3ZXS4, F1R6I3, F6R2G2, P14605, Q09562, Q32KX5, Q38SD2, Q3TX51, Q3UHC2, Q3UV48, Q3ZC49, Q4R6F0, Q54AX5, Q58A48, Q5G5E0, Q62192, Q65YW8, Q65Z91, Q66HD6, Q6AXL3, Q6GLE8, Q6GM71, Q6R5N8, Q6ZNQ3, Q7Z2Q7, Q86X40, Q8BGI7, Q8C0R9, Q8N456, Q8VDB8, Q96DD0, Q99467, Q99MB1, Q9BYS8

Diamond homologs: A6NM36, Q3UV48

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

104 predictions. Top by Δscore:

Variant	Effect	Δscore
18:7231636:G:GT	donor_gain	0.8100
18:7231314:G:GT	donor_gain	0.7300
18:7231568:GTCC:G	donor_gain	0.6600
18:7231569:TCCT:T	donor_gain	0.6600
18:7231315:A:T	donor_gain	0.6500
18:7231906:ACTG:A	donor_loss	0.6200
18:7231908:TGGTG:T	donor_loss	0.6200
18:7231909:GGTG:G	donor_loss	0.6200
18:7231910:G:A	donor_loss	0.6200
18:7231911:T:A	donor_loss	0.6200
18:7231912:GAGGA:G	donor_loss	0.6200
18:7231713:ACGTG:A	acceptor_gain	0.5900
18:7231913:AGGAT:A	donor_loss	0.5900
18:7231565:G:GT	donor_gain	0.5700
18:7231636:G:T	donor_gain	0.5700
18:7231681:T:A	donor_gain	0.5500
18:7231914:G:C	donor_loss	0.5300
18:7231640:C:G	donor_gain	0.5200
18:7231697:G:GT	donor_gain	0.5200
18:7231817:T:TA	donor_gain	0.5200
18:7231713:ACGT:A	acceptor_gain	0.5000
18:7231714:C:G	acceptor_gain	0.5000
18:7231910:G:GG	donor_gain	0.4900
18:7231813:G:GT	acceptor_gain	0.4700
18:7231717:G:A	acceptor_gain	0.4600
18:7231570:C:A	donor_gain	0.4500
18:7231698:A:T	donor_gain	0.4500
18:7231544:C:G	donor_gain	0.4400
18:7231683:T:A	donor_gain	0.4100
18:7231248:G:GT	donor_gain	0.3900

AlphaMissense

1977 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
18:7231574:A:C	S146R	0.995
18:7231576:C:A	S146R	0.995
18:7231576:C:G	S146R	0.995
18:7231641:T:C	L168P	0.994
18:7231710:T:C	L191S	0.994
18:7231845:T:C	L236P	0.994
18:7231519:C:A	N127K	0.993
18:7231519:C:G	N127K	0.993
18:7231657:C:A	N173K	0.993
18:7231657:C:G	N173K	0.993
18:7231848:T:C	L237P	0.993
18:7231588:C:A	N150K	0.992
18:7231588:C:G	N150K	0.992
18:7231706:T:C	F190L	0.992
18:7231708:C:A	F190L	0.992
18:7231708:C:G	F190L	0.992
18:7231940:G:A	G268R	0.992
18:7231940:G:C	G268R	0.992
18:7231365:T:C	L76P	0.991
18:7231450:C:A	N104K	0.991
18:7231450:C:G	N104K	0.991
18:7231647:T:C	L170P	0.991
18:7231779:T:C	F214S	0.991
18:7231726:T:A	N196K	0.990
18:7231726:T:G	N196K	0.990
18:7231854:T:C	L239P	0.990
18:7231940:G:T	G268W	0.990
18:7231944:T:C	L269P	0.990
18:7231960:C:A	N274K	0.990
18:7231960:C:G	N274K	0.990

dbSNP variants (sampled 300 via entrez): RS1001611063 (18:7229156 A>G), RS1001667207 (18:7231063 C>T), RS1002480757 (18:7232407 G>C,T), RS1002640293 (18:7230067 C>A,T), RS1004435862 (18:7232051 T>TC), RS1004487244 (18:7230191 A>G), RS1005483163 (18:7231611 G>T), RS1005630330 (18:7231114 G>A), RS1006554882 (18:7230245 C>T), RS1006630144 (18:7229142 G>A,C), RS1006636922 (18:7232338 C>T), RS1012299819 (18:7231990 G>A), RS1012790751 (18:7231740 T>C), RS1012807755 (18:7229765 C>T), RS1013146239 (18:7229475 C>A)

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

1 associations (top):

Study	Trait	p-value
GCST010566_12	Benign childhood epilepsy with centro-temporal spikes	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	1

Clinical trials (associated diseases)

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