LRRC27

Summary

LRRC27 (leucine rich repeat containing 27, HGNC:29346) is a protein-coding gene on chromosome 10q26.3, encoding Leucine-rich repeat-containing protein 27 (Q9C0I9).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 127 total
• MANE Select transcript: NM_030626

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29346
Approved symbol	LRRC27
Name	leucine rich repeat containing 27
Location	10q26.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1674
Ensembl gene	ENSG00000148814
Ensembl biotype	protein_coding
Entrez	80313

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 9 protein_coding, 8 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000344079, ENST00000368612, ENST00000368613, ENST00000368614, ENST00000450442, ENST00000462656, ENST00000472387, ENST00000472556, ENST00000475747, ENST00000476889, ENST00000487000, ENST00000489204, ENST00000490055, ENST00000625755, ENST00000885091, ENST00000885092, ENST00000930529, ENST00000962088

RefSeq mRNA: 5 — MANE Select: NM_030626 NM_001143757, NM_001143758, NM_001143759, NM_001309474, NM_030626

CCDS: CCDS31316, CCDS44495, CCDS44496

Canonical transcript exons

ENST00000368614 — 11 exons

Exon	Start	End
ENSE00001833285	132332193	132332256
ENSE00001904678	132375066	132381508
ENSE00003503200	132365424	132365550
ENSE00003514318	132333477	132333734
ENSE00003535702	132347984	132348356
ENSE00003544844	132344498	132344650
ENSE00003576796	132361457	132361575
ENSE00003592285	132355790	132355886
ENSE00003631335	132351607	132351753
ENSE00003670247	132342213	132342271
ENSE00003686432	132337565	132337695

Expression profiles

Bgee: expression breadth ubiquitous, 201 present calls, max score 97.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.4658 / max 190.8089, expressed in 1683 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107707	4.7278	1596
206063	0.3517	186
107709	0.1917	81
107710	0.0987	35
107708	0.0960	24

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.11	gold quality
left testis	UBERON:0004533	96.82	gold quality
right testis	UBERON:0004534	96.59	gold quality
testis	UBERON:0000473	93.77	gold quality
right uterine tube	UBERON:0001302	92.76	gold quality
cortical plate	UBERON:0005343	90.14	gold quality
ventricular zone	UBERON:0003053	88.49	gold quality
adenohypophysis	UBERON:0002196	86.83	gold quality
ganglionic eminence	UBERON:0004023	86.40	gold quality
granulocyte	CL:0000094	86.30	gold quality
right frontal lobe	UBERON:0002810	86.24	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.23	gold quality
anterior cingulate cortex	UBERON:0009835	86.23	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.12	gold quality
sural nerve	UBERON:0015488	85.64	gold quality
prefrontal cortex	UBERON:0000451	85.40	gold quality
hypothalamus	UBERON:0001898	84.61	gold quality
nucleus accumbens	UBERON:0001882	84.60	gold quality
amygdala	UBERON:0001876	84.49	gold quality
pituitary gland	UBERON:0000007	84.43	gold quality
caudate nucleus	UBERON:0001873	84.38	gold quality
putamen	UBERON:0001874	83.53	gold quality
left lobe of thyroid gland	UBERON:0001120	83.35	gold quality
spleen	UBERON:0002106	83.31	gold quality
right lobe of thyroid gland	UBERON:0001119	83.23	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.19	gold quality
neocortex	UBERON:0001950	82.98	gold quality
metanephros cortex	UBERON:0010533	82.97	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.87	gold quality
thyroid gland	UBERON:0002046	82.87	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

188 targeting LRRC27, 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-4713-3P	100.00	65.92	505
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-651-3P	99.94	73.48	5177

Literature-anchored findings (GeneRIF, showing 1)

• Exploring the Novel Susceptibility Gene Variants for Primary Open-Angle Glaucoma in East Asian Cohorts: The GLAU-GENDISK Study. (PMID:31937794)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lrrc27	ENSMUSG00000015980
rattus_norvegicus	Lrrc27	ENSRNOG00000017538

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), 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), LRRC30 (ENSG00000206422), LRRC69 (ENSG00000214954), LRRD1 (ENSG00000240720)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 27 — Q9C0I9 (reviewed: Q9C0I9)

All UniProt accessions (2): Q9C0I9, A0A140VJN2

Isoforms (4)

UniProt ID	Names	Canonical?
Q9C0I9-1	1	yes
Q9C0I9-2	2
Q9C0I9-3	3
Q9C0I9-4	4

RefSeq proteins (5): NP_001137229, NP_001137230, NP_001137231, NP_001296403, NP_085129* (*=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: PF13855

UniProt features (16 total): repeat 5, splice variant 4, sequence conflict 2, region of interest 2, chain 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C0I9-F1	63.30	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): COATES_MACROPHAGE_M1_VS_M2_DN, LEIN_MEDULLA_MARKERS, MARSON_BOUND_BY_FOXP3_STIMULATED, GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEN_METABOLIC_SYNDROM_NETWORK, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, YANG_BCL3_TARGETS_UP, ALKBH3_TARGET_GENES, CBX5_TARGET_GENES, CEBPZ_TARGET_GENES, CREBL2_TARGET_GENES, FOXJ2_TARGET_GENES, FOXN3_TARGET_GENES, HES2_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

702 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC27	C3orf22	Q8N5N4	506
LRRC27	RNASE12	Q5GAN4	447
LRRC27	ARHGAP22	Q7Z5H3	447
LRRC27	C12orf56	Q8IXR9	447
LRRC27	SMIM17	P0DL12	437
LRRC27	JAKMIP3	Q5VZ66	431
LRRC27	CCDC144A	A2RUR9	424
LRRC27	SH2D7	A6NKC9	419
LRRC27	C1orf167	Q5SNV9	418
LRRC27	CC2D2B	Q6DHV5	418
LRRC27	C22orf42	Q6IC83	417
LRRC27	ANKRD62	A6NC57	416
LRRC27	LRRC66	Q68CR7	410
LRRC27	SPDYE4	A6NLX3	399
LRRC27	CLPSL1	A2RUU4	395

IntAct

6 interactions, top by confidence:

A	B	Type	Score
LRRC27	HMOX1	psi-mi:“MI:0914”(association)	0.530
LRRC27	H2AC4	psi-mi:“MI:0915”(physical association)	0.400
LRRC27		psi-mi:“MI:0915”(physical association)	0.400
LRRC27	SNRNP200	psi-mi:“MI:0914”(association)	0.350

BioGRID (33): HMOX1 (Affinity Capture-MS), MCM8 (Affinity Capture-MS), SCRIB (Affinity Capture-MS), IFT52 (Affinity Capture-MS), LRRC40 (Affinity Capture-MS), POLA2 (Affinity Capture-MS), WDR19 (Affinity Capture-MS), BBS7 (Affinity Capture-MS), PJA1 (Affinity Capture-MS), LRRC27 (Affinity Capture-RNA), LRRC27 (Affinity Capture-MS), LRRC27 (Two-hybrid), LRRC27 (Proximity Label-MS), LRRC27 (Negative Genetic), LRRC27 (Affinity Capture-RNA)

ESM2 similar proteins: A5PKK7, A8E4X8, B1H222, Q13625, Q28C41, Q2HJA5, Q2KHX9, Q3B7M3, Q499E4, Q4KMA0, Q4V891, Q571B6, Q5M834, Q5RDH2, Q5T7V8, Q5U465, Q5XI03, Q5XIA0, Q5XJA2, Q5ZKM0, Q62036, Q6NRH3, Q6NVC9, Q6PCG6, Q6TYB5, Q7T320, Q7TNY7, Q7ZWE6, Q86XL3, Q8BRM2, Q8BVV7, Q8CG79, Q8IYY4, Q8K3I4, Q8N9B5, Q8NFW9, Q8TF30, Q8VCS6, Q91WZ8, Q96GE4

Diamond homologs: Q80YS5, Q9C0I9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	87
Likely benign	16
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2381 predictions. Top by Δscore:

Variant	Effect	Δscore
10:132333735:G:GG	donor_gain	1.0000
10:132337558:A:AG	acceptor_gain	1.0000
10:132337558:AT:A	acceptor_gain	1.0000
10:132337558:ATG:A	acceptor_gain	1.0000
10:132337559:T:G	acceptor_gain	1.0000
10:132337559:T:TA	acceptor_gain	1.0000
10:132344493:T:A	acceptor_gain	1.0000
10:132344495:CAGG:C	acceptor_loss	1.0000
10:132344496:A:AG	acceptor_gain	1.0000
10:132344496:AG:A	acceptor_gain	1.0000
10:132344497:G:GG	acceptor_gain	1.0000
10:132344497:GG:G	acceptor_gain	1.0000
10:132344497:GGGA:G	acceptor_gain	1.0000
10:132344609:GGGC:G	donor_gain	1.0000
10:132344648:AAG:A	donor_loss	1.0000
10:132344650:GGTT:G	donor_loss	1.0000
10:132344652:T:G	donor_loss	1.0000
10:132344659:G:GT	donor_gain	1.0000
10:132347982:AGAG:A	acceptor_gain	1.0000
10:132347983:GAGG:G	acceptor_gain	1.0000
10:132351605:A:AG	acceptor_gain	1.0000
10:132351606:G:GG	acceptor_gain	1.0000
10:132351750:GACG:G	donor_gain	1.0000
10:132351754:G:GG	donor_gain	1.0000
10:132351754:G:T	donor_loss	1.0000
10:132351755:T:A	donor_loss	1.0000
10:132365422:A:AG	acceptor_gain	1.0000
10:132365423:G:GA	acceptor_gain	1.0000
10:132365423:GT:G	acceptor_gain	1.0000
10:132365423:GTGC:G	acceptor_gain	1.0000

AlphaMissense

3449 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:132342257:T:C	L129S	0.991
10:132342218:T:C	L116S	0.987
10:132337569:T:C	L72S	0.986
10:132342227:T:C	L119S	0.984
10:132342243:T:A	N124K	0.984
10:132342243:T:G	N124K	0.984
10:132344548:T:C	F151L	0.984
10:132344550:C:A	F151L	0.984
10:132344550:C:G	F151L	0.984
10:132337647:T:C	L98P	0.982
10:132337657:T:A	N101K	0.982
10:132337657:T:G	N101K	0.982
10:132337662:T:C	I103T	0.979
10:132337641:T:C	L96P	0.978
10:132344596:T:C	F167L	0.978
10:132344598:C:A	F167L	0.978
10:132344598:C:G	F167L	0.978
10:132348214:T:C	F262L	0.978
10:132348216:T:A	F262L	0.978
10:132348216:T:G	F262L	0.978
10:132337575:T:C	L74P	0.976
10:132344538:C:G	C147W	0.976
10:132337647:T:A	L98H	0.974
10:132342241:A:G	N124D	0.973
10:132342233:T:C	L121S	0.972
10:132337656:A:T	N101I	0.971
10:132342241:A:T	N124Y	0.969
10:132344536:T:C	C147R	0.968
10:132337613:T:C	F87L	0.965
10:132337615:T:A	F87L	0.965

dbSNP variants (sampled 300 via entrez): RS1000012358 (10:132331176 G>A), RS1000022984 (10:132371343 C>T), RS1000045057 (10:132330810 TA>T,TAA), RS1000070798 (10:132375797 C>T), RS1000082783 (10:132336656 A>C), RS1000162533 (10:132351633 T>A), RS1000178512 (10:132366195 G>A), RS1000209432 (10:132365920 C>G,T), RS1000212496 (10:132359218 G>A,T), RS1000266597 (10:132336347 A>C), RS1000278242 (10:132351483 AGTC>A), RS1000294243 (10:132342441 C>T), RS1000364669 (10:132381434 C>T), RS1000371219 (10:132376917 G>A), RS1000434109 (10:132328069 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

5 associations (top):

Study	Trait	p-value
GCST007326_31	Number of sexual partners	1.000000e-10
GCST007335_20	Age at first sexual intercourse	1.000000e-08
GCST010119_1	Glaucoma (primary open-angle)	1.000000e-07
GCST011125_19	Caffeine consumption from coffee	7.000000e-09
GCST90000047_214	Age at first sexual intercourse	1.000000e-15

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009749	age at first sexual intercourse measurement
EFO:0006781	coffee consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases methylation	2
Aflatoxin B1	increases methylation	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
naringenin	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
sodium arsenite	decreases expression	1
hydroquinone	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	increases reaction, affects binding	1
jinfukang	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Cisplatin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Estradiol	affects expression	1
Lead	affects splicing	1
Pesticides	affects methylation	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
tert-Butylhydroperoxide	increases methylation	1

Clinical trials (associated diseases)

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