LRRC36

Summary

LRRC36 (leucine rich repeat containing 36, HGNC:25615) is a protein-coding gene on chromosome 16q22.1, encoding Leucine-rich repeat-containing protein 36 (Q1X8D7).

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_018296

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25615
Approved symbol	LRRC36
Name	leucine rich repeat containing 36
Location	16q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11004
Ensembl gene	ENSG00000159708
Ensembl biotype	protein_coding
Entrez	55282

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 8 nonsense_mediated_decay, 6 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000329956, ENST00000435835, ENST00000561821, ENST00000561948, ENST00000563189, ENST00000563303, ENST00000565019, ENST00000566558, ENST00000567211, ENST00000567723, ENST00000567823, ENST00000568010, ENST00000568804, ENST00000569121, ENST00000569228, ENST00000569499, ENST00000569552, ENST00000570075

RefSeq mRNA: 2 — MANE Select: NM_018296 NM_001161575, NM_018296

CCDS: CCDS32467, CCDS58474

Canonical transcript exons

ENST00000329956 — 14 exons

Exon	Start	End
ENSE00003472999	67378589	67378712
ENSE00003492862	67341957	67342084
ENSE00003496405	67347495	67347591
ENSE00003520373	67382133	67382247
ENSE00003531770	67376727	67376872
ENSE00003567852	67363590	67363714
ENSE00003577154	67367017	67367457
ENSE00003577266	67375247	67375412
ENSE00003621280	67370944	67371242
ENSE00003634107	67346256	67346448
ENSE00003645190	67350202	67350290
ENSE00003789961	67365304	67365355
ENSE00003841346	67384870	67385204
ENSE00003841406	67326815	67326932

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 94.53.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2569 / max 50.5215, expressed in 78 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154616	0.1212	32
154617	0.0719	18
154618	0.0455	23
154620	0.0113	4
154619	0.0070	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	94.53	gold quality
right testis	UBERON:0004534	94.35	gold quality
testis	UBERON:0000473	91.72	gold quality
right uterine tube	UBERON:0001302	90.55	gold quality
sperm	CL:0000019	89.42	gold quality
male germ cell	CL:0000015	88.48	gold quality
adult organism	UBERON:0007023	86.02	gold quality
epithelium of bronchus	UBERON:0002031	84.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.56	gold quality
bronchial epithelial cell	CL:0002328	84.36	gold quality
bronchus	UBERON:0002185	84.00	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.91	gold quality
right lung	UBERON:0002167	81.43	gold quality
pancreatic ductal cell	CL:0002079	79.68	silver quality
lung	UBERON:0002048	78.95	gold quality
placenta	UBERON:0001987	78.13	gold quality
oviduct epithelium	UBERON:0004804	77.28	gold quality
tongue squamous epithelium	UBERON:0006919	76.97	gold quality
upper lobe of left lung	UBERON:0008952	76.03	gold quality
upper lobe of lung	UBERON:0008948	75.84	gold quality
epithelial cell of pancreas	CL:0000083	74.78	gold quality
fallopian tube	UBERON:0003889	74.09	gold quality
epithelium of nasopharynx	UBERON:0001951	73.67	silver quality
lower lobe of lung	UBERON:0008949	73.43	silver quality
olfactory segment of nasal mucosa	UBERON:0005386	73.26	gold quality
type B pancreatic cell	CL:0000169	72.36	gold quality
visceral pleura	UBERON:0002401	72.20	gold quality
islet of Langerhans	UBERON:0000006	71.82	gold quality
olfactory bulb	UBERON:0002264	71.44	gold quality
nasal cavity mucosa	UBERON:0001826	71.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting LRRC36, 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-2115-3P	99.31	69.68	2026
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-4800-5P	97.22	65.91	324

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrrc36	ENSMUSG00000054320
rattus_norvegicus	Lrrc36	ENSRNOG00000016854

Paralogs (1): CEP72 (ENSG00000112877)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 36 — Q1X8D7 (reviewed: Q1X8D7)

Alternative names: ROR gamma-binding protein 70

All UniProt accessions (10): Q1X8D7, H3BND7, H3BNV0, H3BQI9, H3BRB2, H3BRP7, H3BS33, H3BSQ6, J3QRT0, J3QSG3

Isoforms (3)

UniProt ID	Names	Canonical?
Q1X8D7-1	1	yes
Q1X8D7-2	2
Q1X8D7-3	3

RefSeq proteins (2): NP_001155047, NP_060766* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR055320	CEP72-like	Family

Pfam: PF14580

UniProt features (18 total): splice variant 5, sequence variant 3, repeat 2, region of interest 2, compositionally biased region 2, chain 1, sequence conflict 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q1X8D7-F1	55.05	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, chr16q22, AP2_Q3, AP2GAMMA_01, E2A_Q2, ATGGYGGA_UNKNOWN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, CHYLA_CBFA2T3_TARGETS_DN, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12, PRC1_BMI_UP.V1_DN, ZNF2_TARGET_GENES, ZNF274_TARGET_GENES, ZNF512_TARGET_GENES, ZNF843_TARGET_GENES

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

358 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC36	C16orf86	Q6ZW13	478
LRRC36	KCTD19	Q17RG1	475
LRRC36	MS4A5	Q9H3V2	435
LRRC36	ZNF391	Q9UJN7	400
LRRC36	SPATA31G1	Q5VYM1	380
LRRC36	ZDHHC1	Q8WTX9	373
LRRC36	TSNAXIP1	Q2TAA8	370
LRRC36	C5orf34	Q96MH7	359
LRRC36	CCDC13	Q8IYE1	349
LRRC36	TMEM125	Q96AQ2	348
LRRC36	TCEAL3	Q969E4	336
LRRC36	PNLIPRP3	Q17RR3	324
LRRC36	ZNF804B	A4D1E1	322
LRRC36	IER5L	Q5T953	307
LRRC36	PARD6A	Q9NPB6	305

IntAct

8 interactions, top by confidence:

A	B	Type	Score
LRRC36	TEX11	psi-mi:“MI:0915”(physical association)	0.560
LRRC36	SUCLA2	psi-mi:“MI:0915”(physical association)	0.400
LRRC36	H1-1	psi-mi:“MI:0915”(physical association)	0.400
LRRC36	TBL1X	psi-mi:“MI:0914”(association)	0.350
LRRC36	TEX11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): ISCA1 (Affinity Capture-MS), SNX27 (Affinity Capture-MS), SUFU (Affinity Capture-MS), GOLGA3 (Affinity Capture-MS), TBL1X (Affinity Capture-MS), CNDP2 (Affinity Capture-MS), HSPA9 (Affinity Capture-MS), LRRC36 (Two-hybrid), LRRC36 (Proximity Label-MS), SUCLA2 (Proximity Label-MS), SUGT1 (Affinity Capture-MS), SNX27 (Affinity Capture-MS), SUFU (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), CNDP2 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LFM6, A0A1B0GVH6, A0A1L8H8C0, A0A2K1JJ00, A0JMD2, A2ARZ3, A2AWL7, A4IGV6, A6H5Y1, D3ZJ47, E9Q309, F1QPR4, F5H4B4, H0WFA5, O14513, O35413, O94875, P0CAX8, P48437, Q12912, Q15468, Q1LXZ9, Q1X8D7, Q28FG2, Q3UTJ2, Q3ZBS1, Q499E5, Q49A88, Q4V7H1, Q5T5U3, Q5VT06, Q62417, Q62770, Q69Z38, Q6DFB0, Q80TY4, Q8BLN6, Q8CB14, Q8IWI9, Q8K0T7

Diamond homologs: B6CZ40, B6CZ45, B6CZ54, B6CZ61, D4AC13, O35125, O43822, P34390, Q1X8D7, Q28CU0, Q32KP2, Q3UVD5, Q3V0M2, Q53EV4, Q5EAD8, Q8C6G1, Q96E66, Q9DAK8, Q9HBX8, Q9U1H9, B3NLX1, B4GT53, B4P6W7, B6D5P1, B6D5P3, B6D5P6, Q09JZ4, Q16RY9, Q29KL8, Q3SYS4, Q6AYH9, Q7PK92, Q7ZV84, Q8INT5, Q8NEP3, Q9D2H9, Q9D3R3, Q501X2, Q8CDN9, Q9BLB6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	83
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2377 predictions. Top by Δscore:

Variant	Effect	Δscore
16:67372665:G:GT	donor_gain	1.0000
16:67375409:CTCGG:C	donor_loss	1.0000
16:67375410:TCGG:T	donor_loss	1.0000
16:67375413:G:GC	donor_loss	1.0000
16:67375413:G:GG	donor_gain	1.0000
16:67375414:TGAG:T	donor_loss	1.0000
16:67375415:GAGT:G	donor_loss	1.0000
16:67378580:A:AG	acceptor_gain	1.0000
16:67378581:A:G	acceptor_gain	1.0000
16:67346318:A:AG	acceptor_gain	0.9900
16:67346319:G:GG	acceptor_gain	0.9900
16:67346391:A:T	donor_gain	0.9900
16:67363587:C:G	acceptor_gain	0.9900
16:67375243:T:TA	acceptor_gain	0.9900
16:67378585:A:AG	acceptor_gain	0.9900
16:67378585:AAAG:A	acceptor_gain	0.9900
16:67378586:A:G	acceptor_gain	0.9900
16:67378588:GGAAA:G	acceptor_gain	0.9900
16:67378709:TATGG:T	donor_loss	0.9900
16:67378710:ATGGT:A	donor_loss	0.9900
16:67378711:TGGTA:T	donor_loss	0.9900
16:67378713:G:GT	donor_loss	0.9900
16:67378714:TA:T	donor_loss	0.9900
16:67378715:AAGTT:A	donor_loss	0.9900
16:67382112:T:TA	acceptor_gain	0.9900
16:67382245:GAG:G	donor_gain	0.9900
16:67384860:T:A	acceptor_gain	0.9900
16:67384861:G:A	acceptor_gain	0.9900
16:67347493:A:AG	acceptor_gain	0.9800
16:67347494:G:GG	acceptor_gain	0.9800

AlphaMissense

4899 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:67346287:T:C	L77P	1.000
16:67342050:T:C	L55S	0.999
16:67342056:T:C	L57S	0.999
16:67342066:T:A	N60K	0.999
16:67342066:T:G	N60K	0.999
16:67346303:C:A	N82K	0.999
16:67346303:C:G	N82K	0.999
16:67346335:T:C	L93P	0.999
16:67346362:T:C	L102P	0.999
16:67346368:T:C	L104S	0.999
16:67346378:T:A	N107K	0.999
16:67346378:T:G	N107K	0.999
16:67346383:T:A	V109D	0.999
16:67346416:C:A	A120D	0.999
16:67347531:C:A	A143D	0.999
16:67341983:G:A	G33R	0.998
16:67341983:G:C	G33R	0.998
16:67342041:T:A	L52H	0.998
16:67342064:A:G	N60D	0.998
16:67342065:A:T	N60I	0.998
16:67346256:G:A	G67R	0.998
16:67346256:G:C	G67R	0.998
16:67346278:T:A	L74H	0.998
16:67346287:T:A	L77Q	0.998
16:67346302:A:T	N82I	0.998
16:67346371:G:C	R105T	0.998
16:67346371:G:T	R105I	0.998
16:67346372:A:C	R105S	0.998
16:67346372:A:T	R105S	0.998
16:67346374:T:C	L106P	0.998

dbSNP variants (sampled 300 via entrez): RS1000032410 (16:67373386 G>A), RS1000188109 (16:67345637 A>G), RS1000261016 (16:67343595 T>C), RS1000261454 (16:67380896 T>A,C), RS1000297597 (16:67324985 G>C), RS1000471328 (16:67330115 C>T), RS1000479167 (16:67334683 C>T), RS1000486541 (16:67351337 C>T), RS1000636988 (16:67343222 C>G,T), RS1000772788 (16:67353230 A>G), RS1000879075 (16:67366324 T>A,G), RS1000896022 (16:67358754 A>G), RS1000926857 (16:67343537 A>G), RS1000955220 (16:67356732 A>G), RS1000963961 (16:67364076 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

15 associations (top):

Study	Trait	p-value
GCST004562_153	Waist circumference adjusted for body mass index	4.000000e-09
GCST004563_30	Waist circumference adjusted for BMI (joint analysis main effects and physical activity interaction)	2.000000e-08
GCST004564_7	Waist circumference adjusted for BMI in active individuals	8.000000e-08
GCST007483_14	Waist-to-hip ratio adjusted for BMI (additive genetic model)	6.000000e-13
GCST007483_17	Waist-to-hip ratio adjusted for BMI (additive genetic model)	4.000000e-13
GCST007487_30	Waist-to-hip ratio adjusted for BMI (additive genetic model)	7.000000e-11
GCST007487_35	Waist-to-hip ratio adjusted for BMI (additive genetic model)	4.000000e-11
GCST007492_8	Waist-to-hip ratio adjusted for BMI (additive genetic model)	6.000000e-06
GCST007492_9	Waist-to-hip ratio adjusted for BMI (additive genetic model)	2.000000e-06
GCST007500_24	Waist-to-hip ratio adjusted for BMI (additive genetic model)	4.000000e-09
GCST007500_27	Waist-to-hip ratio adjusted for BMI (additive genetic model)	1.000000e-08
GCST007502_23	Waist-to-hip ratio adjusted for BMI (additive genetic model)	3.000000e-09
GCST007502_24	Waist-to-hip ratio adjusted for BMI (additive genetic model)	8.000000e-09
GCST010002_113	Refractive error	2.000000e-14
GCST010571_65	Autoimmune thyroid disease	2.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007789	BMI-adjusted waist circumference
EFO:0008002	physical activity measurement
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Nickel	decreases expression	2
propionaldehyde	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Phthalic Acids	increases methylation	1
Rotenone	increases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Asbestos, Crocidolite	affects methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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