LRRC9

Summary

LRRC9 (leucine rich repeat containing 9, HGNC:19848) is a protein-coding gene on chromosome 14q23.1, encoding Leucine-rich repeat-containing protein 9 (Q6ZRR7).

Predicted to enable U2 snRNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in cytoplasm.

Source: NCBI Gene 341883 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001395648

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19848
Approved symbol	LRRC9
Name	leucine rich repeat containing 9
Location	14q23.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ46156
Ensembl gene	ENSG00000131951
Ensembl biotype	protein_coding
Entrez	341883

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 nonsense_mediated_decay, 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000254271, ENST00000445360, ENST00000454474, ENST00000562571, ENST00000568404, ENST00000570145, ENST00000644811, ENST00000647410

RefSeq mRNA: 2 — MANE Select: NM_001395648 NM_001355272, NM_001395648

CCDS: CCDS86397

Canonical transcript exons

ENST00000570145 — 33 exons

Exon	Start	End
ENSE00001307866	59977225	59977347
ENSE00001314079	59978017	59978132
ENSE00001631059	59997656	59997847
ENSE00001632544	60016660	60016790
ENSE00001635285	60031995	60032063
ENSE00001639729	59999101	59999226
ENSE00001651281	60006397	60006617
ENSE00001659868	59981848	59982060
ENSE00001665728	60001966	60002100
ENSE00001667894	60003621	60003798
ENSE00001671327	60008092	60008214
ENSE00001673414	59966589	59966765
ENSE00001724146	59985105	59985224
ENSE00001742416	59928268	59928486
ENSE00001742862	59967096	59967213
ENSE00001756429	59960914	59961045
ENSE00001767842	59974576	59974708
ENSE00001790581	60018371	60018479
ENSE00001800107	59959818	59960014
ENSE00002597827	59927911	59927991
ENSE00002617462	59920144	59920273
ENSE00003469888	59938390	59938572
ENSE00003534143	60027884	60028101
ENSE00003611325	60022734	60022870
ENSE00003618673	59944589	59944744
ENSE00003623011	59931969	59932039
ENSE00003637882	60057878	60058022
ENSE00003650774	59931619	59931682
ENSE00003660353	59930918	59931058
ENSE00003663343	60019121	60019260
ENSE00003689040	60053065	60053205
ENSE00003821311	60062011	60062179
ENSE00003996971	60063323	60066817

Expression profiles

Bgee: expression breadth ubiquitous, 101 present calls, max score 85.07.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1913 / max 20.8472, expressed in 88 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
139854	0.1913	88

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.07	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.39	gold quality
testis	UBERON:0000473	73.29	gold quality
ventricular zone	UBERON:0003053	73.19	gold quality
left testis	UBERON:0004533	73.12	gold quality
right testis	UBERON:0004534	72.84	gold quality
corpus callosum	UBERON:0002336	70.92	gold quality
right uterine tube	UBERON:0001302	64.88	gold quality
islet of Langerhans	UBERON:0000006	64.29	gold quality
ganglionic eminence	UBERON:0004023	62.61	gold quality
adrenal tissue	UBERON:0018303	61.95	gold quality
pituitary gland	UBERON:0000007	60.34	gold quality
adenohypophysis	UBERON:0002196	60.28	gold quality
superior frontal gyrus	UBERON:0002661	57.94	gold quality
prefrontal cortex	UBERON:0000451	56.72	gold quality
fallopian tube	UBERON:0003889	55.81	gold quality
hypothalamus	UBERON:0001898	54.27	gold quality
nucleus accumbens	UBERON:0001882	52.72	gold quality
frontal cortex	UBERON:0001870	52.57	gold quality
cortical plate	UBERON:0005343	52.57	gold quality
caudate nucleus	UBERON:0001873	51.03	gold quality
calcaneal tendon	UBERON:0003701	50.68	gold quality
pancreas	UBERON:0001264	50.43	gold quality
cerebral cortex	UBERON:0000956	50.17	gold quality
prostate gland	UBERON:0002367	49.72	gold quality
Ammon’s horn	UBERON:0001954	49.57	gold quality
brain	UBERON:0000955	49.52	gold quality
Brodmann (1909) area 9	UBERON:0013540	49.50	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	48.35	gold quality
liver	UBERON:0002107	48.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.78

Regulation

Is transcription factor: no

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc9	ENSDARG00000054352
mus_musculus	Lrrc9	ENSMUSG00000021090
rattus_norvegicus	Lrrc9	ENSRNOG00000005409
drosophila_melanogaster	TbCMF46	FBGN0032163
drosophila_melanogaster	Ppr-Y	FBGN0046697

Paralogs (13): LRRC23 (ENSG00000010626), LRRC61 (ENSG00000127399), DNAAF11 (ENSG00000129295), LRRCC1 (ENSG00000133739), LRRC49 (ENSG00000137821), LRRC46 (ENSG00000141294), DNAAF1 (ENSG00000154099), LRGUK (ENSG00000155530), LRRC43 (ENSG00000158113), LRRIQ3 (ENSG00000162620), DRC3 (ENSG00000171962), PPP1R42 (ENSG00000178125), CEP97 (ENSG00000182504)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 9 — Q6ZRR7 (reviewed: Q6ZRR7)

All UniProt accessions (4): A0A2R8YDI6, Q6ZRR7, H3BUB1, H3BUS4

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZRR7-1	1	yes
Q6ZRR7-2	2

RefSeq proteins (2): NP_001342201, NP_001382577* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR025875	Leu-rich_rpt_4	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR050836	SDS22/Internalin_LRR	Family

Pfam: PF12799, PF13855, PF14580

UniProt features (36 total): repeat 30, splice variant 2, sequence conflict 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZRR7-F1	80.98	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): chr14q23, CTGTTAC_MIR194, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_CEREBELLUM_ASTROCYTES, DESCARTES_FETAL_CEREBRUM_ASTROCYTES, DESCARTES_FETAL_LIVER_HEPATOBLASTS, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, GSE12003_4D_VS_8D_CULTURE_BM_PROGENITOR_DN, GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_6H_UP, GSE5589_WT_VS_IL10_KO_LPS_STIM_MACROPHAGE_180MIN_DN, GSE40274_CTRL_VS_FOXP3_AND_PBX1_TRANSDUCED_ACTIVATED_CD4_TCELL_DN, GSE40274_CTRL_VS_FOXP3_AND_SATB1_TRANSDUCED_ACTIVATED_CD4_TCELL_DN, GSE33292_DN3_THYMOCYTE_VS_TCF1_KO_TCELL_LYMPHOMA_DN, TCTCTCC_MIR185

GO Biological Process (1): mRNA splicing, via spliceosome (GO:0000398)

GO Molecular Function (2): protein binding (GO:0005515), U2 snRNA binding (GO:0030620)

GO Cellular Component (2): cytoplasm (GO:0005737), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
binding	1
snRNA binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

603 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC9	GOLGA8M	H3BSY2	621
LRRC9	SMIM31	A0A1B0GVY4	611
LRRC9	ZFP36L2	P47974	567
LRRC9	SAMD12	Q8N8I0	529
LRRC9	CDRT4	Q8N9R6	479
LRRC9	SIX6	O95475	473
LRRC9	FERRY3	Q9NQ89	392
LRRC9	EDA	Q92838	387
LRRC9	RPS12	P25398	377
LRRC9	POFUT4	Q495W5	343
LRRC9	TULP4	Q9NRJ4	329
LRRC9	ARHGAP44	Q17R89	329
LRRC9	TYMP	P19971	329
LRRC9	NEURL4	Q96JN8	329
LRRC9	GNS	P15586	322
LRRC9	SHISA3	A0PJX4	322

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LRRC9	HSPD1	psi-mi:“MI:0915”(physical association)	0.400

ESM2 similar proteins: A0JM56, A0M8T3, A1X154, A4D7T3, A6NJI9, Q008S8, Q00PJ3, Q07DV3, Q07DX6, Q07DY6, Q07DZ7, Q07E17, Q07E30, Q07E43, Q09YH1, Q09YI3, Q09YJ5, Q09YK6, Q09YN0, Q0VD31, Q108U1, Q2IBB1, Q2IBB4, Q2IBE3, Q2IBF5, Q2IBG0, Q2QL84, Q2QLA4, Q2QLB5, Q2QLC6, Q2QLG0, Q2QLH1, Q32NR9, Q5PPX0, Q5ZLG9, Q6DCF6, Q6GQN5, Q6PJI9, Q6ZRR7, Q8BH70

Diamond homologs: A0JM56, Q08963, Q6ZRR7, Q8CDN9, A0A1L8G016, B3DH20, B6CZ40, B6CZ45, B6CZ54, B6CZ61, O35125, O43822, P09661, P34390, P43333, P57784, Q09JZ4, Q16RY9, Q28CU0, Q28FY0, Q32KP2, Q4R8Y8, Q4V8C9, Q53EV4, Q5EAD8, Q6AYH9, Q6NRC9, Q7PK92, Q8IYG6, Q96E66, Q9BLB6, Q9DAK8, A8WHP9, B0M0P8, B1H234, D3ZTV3, F1NUK7, F4J7T6, O02678, O35103

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

5848 predictions. Top by Δscore:

Variant	Effect	Δscore
14:59927909:A:AG	acceptor_gain	1.0000
14:59927910:G:GG	acceptor_gain	1.0000
14:59932037:AAG:A	donor_loss	1.0000
14:59932038:AG:A	donor_loss	1.0000
14:59932039:GGTA:G	donor_loss	1.0000
14:59932040:GT:G	donor_loss	1.0000
14:59944745:G:GG	donor_gain	1.0000
14:59959816:AGTT:A	acceptor_gain	1.0000
14:59959816:AGTTG:A	acceptor_gain	1.0000
14:59959817:G:GA	acceptor_gain	1.0000
14:59959817:GTTG:G	acceptor_gain	1.0000
14:59959817:GTTGG:G	acceptor_gain	1.0000
14:59959953:A:G	donor_gain	1.0000
14:59959984:GG:G	donor_gain	1.0000
14:59959985:GG:G	donor_gain	1.0000
14:59960010:GATGA:G	donor_gain	1.0000
14:59960011:A:AG	donor_gain	1.0000
14:59960011:A:G	donor_gain	1.0000
14:59960013:GA:G	donor_gain	1.0000
14:59960015:G:GG	donor_gain	1.0000
14:59974570:TTGCA:T	acceptor_loss	1.0000
14:59974571:TGCA:T	acceptor_loss	1.0000
14:59974572:GCA:G	acceptor_loss	1.0000
14:59974573:CA:C	acceptor_loss	1.0000
14:59974574:A:AG	acceptor_gain	1.0000
14:59974574:A:G	acceptor_loss	1.0000
14:59974574:AGCT:A	acceptor_gain	1.0000
14:59974575:G:C	acceptor_loss	1.0000
14:59974575:G:GT	acceptor_gain	1.0000
14:59974575:GC:G	acceptor_gain	1.0000

AlphaMissense

732 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:59928395:T:C	L59P	0.989
14:59928461:T:C	L81P	0.988
14:59930958:T:C	L103P	0.983
14:59928461:T:A	L81H	0.973
14:59930974:T:A	N108K	0.970
14:59930974:T:G	N108K	0.970
14:59928395:T:A	L59H	0.965
14:59928452:T:A	L78H	0.965
14:59928477:C:G	C86W	0.960
14:59928461:T:G	L81R	0.958
14:59928463:T:A	W82R	0.958
14:59928463:T:C	W82R	0.958
14:59930964:T:C	L105S	0.958
14:59928386:T:C	L56S	0.956
14:59928395:T:G	L59R	0.956
14:59928475:T:C	C86R	0.953
14:59928452:T:C	L78P	0.952
14:59927990:T:C	L16P	0.950
14:59930958:T:A	L103Q	0.948
14:59928376:T:C	F53L	0.947
14:59928378:T:A	F53L	0.947
14:59928378:T:G	F53L	0.947
14:59928279:T:A	N20K	0.946
14:59928279:T:G	N20K	0.946
14:59928377:T:C	F53S	0.944
14:59930958:T:G	L103R	0.944
14:59930949:T:C	L100S	0.943
14:59928329:T:C	L37S	0.942
14:59928401:T:A	I61N	0.933
14:59930979:T:C	I110T	0.932

dbSNP variants (sampled 300 via entrez): RS1000074417 (14:59989259 TGTC>T), RS1000078643 (14:59968205 T>C), RS1000099722 (14:59939166 C>G), RS1000138110 (14:60061128 T>C), RS1000144161 (14:59935565 T>G), RS1000165844 (14:60013388 T>A), RS1000177039 (14:59935991 T>G), RS1000208441 (14:59996013 T>C), RS1000236714 (14:59988826 T>C), RS1000243788 (14:60064417 T>A), RS1000265317 (14:59959774 A>G), RS1000272698 (14:60006105 G>T), RS1000287838 (14:60002802 C>G,T), RS1000298259 (14:59974347 AT>A), RS1000305241 (14:60041903 T>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
kojic acid	increases expression	1
Acetaminophen	increases expression	1

Clinical trials (associated diseases)

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