LRRC63

Summary

LRRC63 (leucine rich repeat containing 63, HGNC:34296) is a protein-coding gene on chromosome 13q14.13, encoding Leucine-rich repeat-containing protein 63 (Q05C16).

Predicted to be involved in intracellular signal transduction. Predicted to be located in membrane.

Source: NCBI Gene 220416 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• MANE Select transcript: NM_001282460

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34296
Approved symbol	LRRC63
Name	leucine rich repeat containing 63
Location	13q14.13
Locus type	gene with protein product
Status	Approved
Aliases	RP11-139H14.4
Ensembl gene	ENSG00000173988
Ensembl biotype	protein_coding
Entrez	220416

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 5 nonsense_mediated_decay, 1 non_stop_decay, 1 retained_intron

ENST00000378805, ENST00000446175, ENST00000595396, ENST00000674570, ENST00000674837, ENST00000674850, ENST00000675008, ENST00000675095, ENST00000675195, ENST00000675912, ENST00000676025, ENST00000676446

RefSeq mRNA: 1 — MANE Select: NM_001282460 NM_001282460

CCDS: CCDS61325

Canonical transcript exons

ENST00000595396 — 10 exons

Exon	Start	End
ENSE00001179759	46250355	46250491
ENSE00001179766	46246527	46246625
ENSE00001179773	46234192	46234349
ENSE00001179795	46227512	46228189
ENSE00001478818	46228665	46228733
ENSE00001478820	46213002	46213119
ENSE00001542753	46261909	46261992
ENSE00001721522	46266733	46266972
ENSE00003978171	46211928	46212259
ENSE00003978172	46276590	46277115

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 85.83.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0547 / max 108.5483, expressed in 304 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135005	0.9799	286
135006	0.0748	35

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.21	gold quality
spinal cord	UBERON:0002240	81.21	gold quality
right uterine tube	UBERON:0001302	78.31	gold quality
right testis	UBERON:0004534	73.90	gold quality
left testis	UBERON:0004533	73.42	gold quality
testis	UBERON:0000473	71.66	gold quality
corpus callosum	UBERON:0002336	69.82	gold quality
cortical plate	UBERON:0005343	69.00	gold quality
substantia nigra	UBERON:0002038	67.00	gold quality
right adrenal gland cortex	UBERON:0035827	64.71	gold quality
midbrain	UBERON:0001891	63.79	gold quality
right adrenal gland	UBERON:0001233	63.33	gold quality
hypothalamus	UBERON:0001898	62.97	gold quality
adrenal tissue	UBERON:0018303	62.15	gold quality
left adrenal gland cortex	UBERON:0035825	61.93	gold quality
left adrenal gland	UBERON:0001234	61.50	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	61.28	gold quality
Brodmann (1909) area 9	UBERON:0013540	61.06	gold quality
adrenal cortex	UBERON:0001235	60.95	gold quality
amygdala	UBERON:0001876	60.58	gold quality
prefrontal cortex	UBERON:0000451	60.07	gold quality
putamen	UBERON:0001874	59.79	gold quality
adrenal gland	UBERON:0002369	59.79	gold quality
ganglionic eminence	UBERON:0004023	59.17	gold quality
Ammon’s horn	UBERON:0001954	58.36	gold quality
caudate nucleus	UBERON:0001873	56.78	gold quality
ventricular zone	UBERON:0003053	56.74	gold quality
granulocyte	CL:0000094	55.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.54

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrrc63	ENSMUSG00000021997
rattus_norvegicus	Lrrc63	ENSRNOG00000038291

Protein

Protein identifiers

Leucine-rich repeat-containing protein 63 — Q05C16 (reviewed: Q05C16)

All UniProt accessions (9): Q05C16, A0A6Q8PF72, A0A6Q8PFF0, A0A6Q8PFU4, A0A6Q8PGP9, A0A6Q8PGX1, A0A6Q8PHN9, A0AA75I522, J3KQU2

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_001269389* (*=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
IPR055414	LRR_R13L4/SHOC2-like	Domain

Pfam: PF23598

UniProt features (12 total): repeat 7, sequence variant 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q05C16-F1	59.74	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, chr13q14, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_129_MOUSE_UP, ZIM3_TARGET_GENES, ZNF577_TARGET_GENES, HBZ_TARGET_GENES, MEF2C_TARGET_GENES, ZSCAN4_TARGET_GENES, ZNF777_TARGET_GENES, NOTCH3_TARGET_GENES, GSE17974_0H_VS_0.5H_IN_VITRO_ACT_CD4_TCELL_DN, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_0.5H_ACT_CD4_TCELL_DN, GSE7768_OVA_WITH_LPS_VS_OVA_WITH_MPL_IMMUNIZED_MOUSE_WHOLE_SPLEEN_6H_DN

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

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular anatomical structure	1
signal transduction	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

466 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC63	CCDC74B	Q96LY2	668
LRRC63	A0A494C0M2	A0A494C0M2	653
LRRC63	ANKRD60	Q9BZ19	606
LRRC63	SPATA31A1	Q5TZJ5	597
LRRC63	C12orf42	Q96LP6	568
LRRC63	FAM47C	Q5HY64	541
LRRC63	TTLL8	A6PVC2	529
LRRC63	MGAT4D	A6NG13	524
LRRC63	CT45A3	P0DMU6	506
LRRC63	ZSCAN16	Q9H4T2	447
LRRC63	KATNIP	O60303	446
LRRC63	MTRNR2L1	P0CJ68	417
LRRC63	PAQR9	Q6ZVX9	390
LRRC63	PRTG	Q2VWP7	387
LRRC63	BEST3	Q8N1M1	366

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LRRC63	HSP90B1	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): LRRC63 (Proximity Label-MS)

ESM2 similar proteins: A1A5R8, A6H694, A6PVS8, B8A5Y1, D3Z6S9, F1MCA7, P62283, P62285, P62287, P62288, P62289, P62290, P62291, P62292, P62293, P62294, P62296, P62297, P62932, P70587, Q05C16, Q14DL3, Q3U3V8, Q3V0J4, Q497N7, Q4R3V2, Q4R739, Q4V8G0, Q53TS8, Q5CZC0, Q5RA75, Q6AXY2, Q6AYL8, Q6P2D8, Q6PUR7, Q7PCK7, Q7T3T8, Q7Z7J5, Q80TE7, Q86WZ0

Diamond homologs: A6H694, Q05C16, Q4V8G0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1970 predictions. Top by Δscore:

Variant	Effect	Δscore
13:46212080:GAGA:G	donor_gain	1.0000
13:46234187:TTTA:T	acceptor_loss	1.0000
13:46234188:TTAG:T	acceptor_loss	1.0000
13:46234189:TA:T	acceptor_loss	1.0000
13:46234190:A:AG	acceptor_gain	1.0000
13:46234191:G:GT	acceptor_gain	1.0000
13:46234316:TC:T	donor_gain	1.0000
13:46234348:AGGT:A	donor_loss	1.0000
13:46234350:G:A	donor_loss	1.0000
13:46234351:T:A	donor_loss	1.0000
13:46212083:A:G	donor_gain	0.9900
13:46212097:GCCA:G	donor_gain	0.9900
13:46212101:G:GG	donor_gain	0.9900
13:46212111:A:T	donor_gain	0.9900
13:46212134:G:T	donor_gain	0.9900
13:46212219:G:GT	donor_gain	0.9900
13:46234191:GGT:G	acceptor_gain	0.9900
13:46234191:GGTC:G	acceptor_gain	0.9900
13:46234191:GGTCT:G	acceptor_gain	0.9900
13:46246623:GAA:G	donor_gain	0.9900
13:46246626:G:GG	donor_gain	0.9900
13:46253886:A:AG	acceptor_gain	0.9900
13:46262001:G:GT	donor_gain	0.9900
13:46266816:A:AG	donor_gain	0.9900
13:46266817:G:GG	donor_gain	0.9900
13:46266855:A:G	donor_gain	0.9900
13:46276588:A:AG	acceptor_gain	0.9900
13:46276589:G:GG	acceptor_gain	0.9900
13:46276589:GCAC:G	acceptor_gain	0.9900
13:46212031:G:GT	donor_gain	0.9800

AlphaMissense

3857 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000021184 (13:46258739 T>C,G), RS1000090483 (13:46276488 A>G), RS1000097596 (13:46229974 G>A), RS1000135799 (13:46210056 T>C), RS1000155285 (13:46212981 T>C), RS1000169654 (13:46255028 T>A), RS1000224142 (13:46255221 T>G), RS1000230350 (13:46223271 G>A,C), RS1000244503 (13:46216973 G>A), RS1000303362 (13:46269542 A>T), RS1000307669 (13:46248251 G>A), RS1000353480 (13:46261327 C>A), RS1000359968 (13:46216504 A>G), RS1000371118 (13:46268523 C>T), RS1000406688 (13:46261752 A>C,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

2 associations (top):

Study	Trait	p-value
GCST003155_30	Systemic lupus erythematosus	6.000000e-07
GCST004033_12	QRS interval (sulfonylurea treatment interaction)	6.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007922	response to sulfonylurea

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
Tobacco Smoke Pollution	decreases expression	1
Triclosan	decreases expression	1

Clinical trials (associated diseases)

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