LRRC31

Summary

LRRC31 (leucine rich repeat containing 31, HGNC:26261) is a protein-coding gene on chromosome 3q26.2, encoding Leucine-rich repeat-containing protein 31 (Q6UY01).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_024727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26261
Approved symbol	LRRC31
Name	leucine rich repeat containing 31
Location	3q26.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23259
Ensembl gene	ENSG00000114248
Ensembl biotype	protein_coding
OMIM	620925
Entrez	79782

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000264676, ENST00000316428, ENST00000397805, ENST00000523069, ENST00000945886, ENST00000945887, ENST00000945888, ENST00000945889, ENST00000945890, ENST00000945891

RefSeq mRNA: 3 — MANE Select: NM_024727 NM_001277127, NM_001277128, NM_024727

CCDS: CCDS43167, CCDS63832, CCDS63833

Canonical transcript exons

ENST00000316428 — 9 exons

Exon	Start	End
ENSE00000780242	169851619	169851786
ENSE00001151774	169848120	169848287
ENSE00002111468	169869633	169869935
ENSE00002138041	169839172	169840313
ENSE00003492786	169860561	169860728
ENSE00003493482	169861670	169861813
ENSE00003648497	169856705	169856872
ENSE00003675803	169854813	169854980
ENSE00003685043	169856336	169856503

Expression profiles

Bgee: expression breadth broad, 78 present calls, max score 89.61.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0464 / max 22.0118, expressed in 18 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
45539	0.0344	13
45540	0.0120	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
rectum	UBERON:0001052	89.61	gold quality
mucosa of transverse colon	UBERON:0004991	86.91	gold quality
colonic mucosa	UBERON:0000317	81.59	gold quality
jejunal mucosa	UBERON:0000399	80.36	gold quality
mucosa of sigmoid colon	UBERON:0004993	79.52	gold quality
transverse colon	UBERON:0001157	75.82	gold quality
duodenum	UBERON:0002114	73.05	gold quality
small intestine Peyer’s patch	UBERON:0003454	69.26	gold quality
small intestine	UBERON:0002108	68.94	gold quality
colonic epithelium	UBERON:0000397	68.70	gold quality
ileal mucosa	UBERON:0000331	68.46	gold quality
ileum	UBERON:0002116	68.42	silver quality
body of stomach	UBERON:0001161	67.28	gold quality
stomach	UBERON:0000945	67.05	gold quality
intestine	UBERON:0000160	66.08	gold quality
large intestine	UBERON:0000059	65.07	gold quality
minor salivary gland	UBERON:0001830	64.44	gold quality
right lobe of liver	UBERON:0001114	64.15	gold quality
colon	UBERON:0001155	64.13	gold quality
cardia of stomach	UBERON:0001162	62.66	gold quality
jejunum	UBERON:0002115	62.43	gold quality
endometrium	UBERON:0001295	61.61	gold quality
mouth mucosa	UBERON:0003729	61.28	gold quality
saliva-secreting gland	UBERON:0001044	60.88	gold quality
liver	UBERON:0002107	60.06	gold quality
fundus of stomach	UBERON:0001160	59.77	gold quality
vermiform appendix	UBERON:0001154	59.45	gold quality
caecum	UBERON:0001153	57.35	gold quality
bronchial epithelial cell	CL:0002328	57.16	silver quality
epithelium of bronchus	UBERON:0002031	56.47	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting LRRC31, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-379-3P	99.69	69.60	1524
HSA-MIR-411-3P	99.69	69.63	1524
HSA-MIR-8061	99.63	69.44	1411
HSA-MIR-9851-3P	99.63	69.68	1110

Literature-anchored findings (GeneRIF, showing 1)

• this report shows that leucine-rich repeat-containing protein 31 (LRRC31) regulates esophageal epithelial barrier function (PMID:26462420)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc31	ENSDARG00000057392
mus_musculus	Lrrc31	ENSMUSG00000074653
rattus_norvegicus	Lrrc31	ENSRNOG00000027971

Protein

Protein identifiers

Leucine-rich repeat-containing protein 31 — Q6UY01 (reviewed: Q6UY01)

All UniProt accessions (2): A0A384N629, Q6UY01

Isoforms (4)

UniProt ID	Names	Canonical?
Q6UY01-1	1	yes
Q6UY01-2	2
Q6UY01-3	3
Q6UY01-4	4

RefSeq proteins (3): NP_001264056, NP_001264057, NP_079003* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR042419	LRC31	Family

Pfam: PF13516

UniProt features (22 total): repeat 9, splice variant 5, sequence variant 3, compositionally biased region 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UY01-F1	85.68	0.71

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN, chr3q26, AGGCACT_MIR5153P, BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP, DOANE_BREAST_CANCER_CLASSES_UP, PRC1_BMI_UP.V1_UP, TAVAZOIE_METASTASIS, KRAS.600_UP.V1_DN, KRAS.KIDNEY_UP.V1_DN, NKX2_2_TARGET_GENES, MIR1277_5P, MIR335_3P, MIR656_3P, MIR3924, MIR6083

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

803 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC31	LRRIQ4	A6NIV6	695
LRRC31	LRRC34	Q8IZ02	621
LRRC31	MYNN	Q9NPC7	583
LRRC31	CAPN14	A8MX76	571
LRRC31	TMEM174	Q8WUU8	557
LRRC31	CEP295NL	Q96MC4	502
LRRC31	XRCC6	P12956	486
LRRC31	XRCC5	P13010	486
LRRC31	ACTRT3	Q9BYD9	479
LRRC31	LRRC32	Q14392	434
LRRC31	DNPEP	Q9ULA0	425
LRRC31	DSG1	Q02413	419
LRRC31	CLRN2	A0PK11	417
LRRC31	LYPD6	Q86Y78	414
LRRC31	WDSUB1	Q8N9V3	402

IntAct

8 interactions, top by confidence:

A	B	Type	Score
CFTR	CNOT1	psi-mi:“MI:0914”(association)	0.480
LRRC31	PARP1	psi-mi:“MI:0915”(physical association)	0.400
LRRC31	TRIP10	psi-mi:“MI:0915”(physical association)	0.400
LRRC31		psi-mi:“MI:0915”(physical association)	0.400
CFTR	POTEF	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350

BioGRID (209): TRIP10 (Affinity Capture-MS), LRRC31 (Affinity Capture-MS), LRRC31 (Proximity Label-MS), XRCC6 (Affinity Capture-Western), XRCC5 (Affinity Capture-Western), ATR (Affinity Capture-Western), LRRC31 (Affinity Capture-Western), LRRC31 (Affinity Capture-Western), LRRC31 (Affinity Capture-Western), LRRC31 (Affinity Capture-Western), ACACA (Affinity Capture-MS), ACTB (Affinity Capture-MS), PARP4 (Affinity Capture-MS), AIM1 (Affinity Capture-MS), SLC25A5 (Affinity Capture-MS)

ESM2 similar proteins: A5PJJ5, A6NHZ5, E9Q5R7, G1T469, G3XA59, P02750, P10775, P13489, P22792, P29315, P59046, P59047, Q14392, Q149C3, Q14BP6, Q15048, Q32PG9, Q3UJB3, Q3V3V9, Q3ZBI5, Q53B87, Q53B88, Q569B5, Q5BK65, Q5DU56, Q5RF01, Q63035, Q640Z9, Q647I9, Q6F5E8, Q6QMY6, Q6UY01, Q6UY18, Q6ZQY2, Q7RTR2, Q86W24, Q86W25, Q86YC3, Q8BMT4, Q8CBR6

Diamond homologs: A1Z198, A6QLE5, B0FPE9, D4A523, D9I2F9, D9I2G1, D9I2G3, D9I2G4, D9I2H0, E9Q5R7, P10775, P13489, P29315, P59044, P59045, P59046, P59047, P79621, Q0GKD5, Q288C4, Q2LKU9, Q2LKV2, Q2LKV5, Q2LKW6, Q647I9, Q6B966, Q6UY01, Q7RTR0, Q86W24, Q86W25, Q86W26, Q86W28, Q8CCN1, Q8HZP9, Q8R4B8, Q8WX94, Q91VI7, Q91WS2, Q96MN2, Q96P20

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1788 predictions. Top by Δscore:

Variant	Effect	Δscore
3:169856501:GACCT:G	acceptor_loss	1.0000
3:169856502:ACCT:A	acceptor_loss	1.0000
3:169856504:C:CC	acceptor_gain	1.0000
3:169856504:C:CG	acceptor_loss	1.0000
3:169856505:T:A	acceptor_loss	1.0000
3:169856698:CACTT:C	donor_loss	1.0000
3:169856699:ACTTA:A	donor_loss	1.0000
3:169856700:CTTA:C	donor_loss	1.0000
3:169856701:TTACC:T	donor_loss	1.0000
3:169856702:TAC:T	donor_loss	1.0000
3:169856703:A:C	donor_loss	1.0000
3:169856703:AC:A	donor_gain	1.0000
3:169856704:C:G	donor_loss	1.0000
3:169856704:CC:C	donor_gain	1.0000
3:169858288:C:CA	donor_gain	1.0000
3:169869629:TTACC:T	donor_loss	1.0000
3:169869630:TACC:T	donor_loss	1.0000
3:169869631:A:AC	donor_gain	1.0000
3:169869631:A:AT	donor_loss	1.0000
3:169869632:C:CC	donor_gain	1.0000
3:169869632:C:CT	donor_loss	1.0000
3:169869632:CCAGT:C	donor_gain	1.0000
3:169840309:CGATG:C	acceptor_gain	0.9900
3:169840312:TG:T	acceptor_gain	0.9900
3:169840314:C:CC	acceptor_gain	0.9900
3:169848134:T:TA	donor_gain	0.9900
3:169856328:TAAC:T	donor_loss	0.9900
3:169856329:AAC:A	donor_loss	0.9900
3:169856330:ACT:A	donor_loss	0.9900
3:169856331:CT:C	donor_loss	0.9900

AlphaMissense

3625 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:169840074:A:G	W523R	0.979
3:169840074:A:T	W523R	0.979
3:169840174:G:C	S489R	0.967
3:169840174:G:T	S489R	0.967
3:169840176:T:G	S489R	0.967
3:169840233:A:G	W470R	0.967
3:169840233:A:T	W470R	0.967
3:169856820:G:C	N180K	0.966
3:169856820:G:T	N180K	0.966
3:169854854:A:G	L317P	0.959
3:169851734:G:C	N348K	0.958
3:169851734:G:T	N348K	0.958
3:169840265:A:G	L459P	0.957
3:169851750:A:G	L343S	0.955
3:169856383:A:G	L259P	0.954
3:169856836:A:G	L175P	0.953
3:169854938:A:G	L289P	0.952
3:169840255:A:C	N462K	0.950
3:169840255:A:T	N462K	0.950
3:169840140:A:G	W501R	0.946
3:169840140:A:T	W501R	0.946
3:169848235:G:C	N404K	0.944
3:169848235:G:T	N404K	0.944
3:169840184:A:G	L486P	0.943
3:169854928:A:C	N292K	0.941
3:169854928:A:T	N292K	0.941
3:169848151:A:C	C432W	0.938
3:169840271:A:G	L457P	0.935
3:169851744:A:G	L345S	0.935
3:169848154:G:C	S431R	0.934

dbSNP variants (sampled 300 via entrez): RS1000175488 (3:169870321 C>G), RS1000247621 (3:169870635 C>A,T), RS1000274929 (3:169842896 GAAAT>G), RS1000438187 (3:169862169 G>A), RS1000482452 (3:169846585 T>G), RS1000510238 (3:169871837 G>A), RS1000635186 (3:169840773 A>C,G), RS1000773735 (3:169865489 T>C), RS1000836040 (3:169863845 A>G), RS1000894334 (3:169855339 C>T), RS1001021576 (3:169848474 TTGAGACAGAGCCTTGCTC>T), RS1001081964 (3:169844253 C>T), RS1001142252 (3:169865264 G>A,T), RS1001381214 (3:169851060 A>C), RS1001451341 (3:169858875 A>G)

Disease associations

OMIM: gene MIM:620925 | 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
GCST90002394_261	Monocyte percentage of white cells	3.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007989	monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	3
Aflatoxin B1	affects expression, decreases expression, decreases methylation	3
Endosulfan	affects cotreatment, decreases expression, increases expression	2
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression, increases expression	2
Cyclosporine	decreases expression	2
bisphenol A	affects cotreatment, affects methylation, decreases methylation	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	increases expression	1
perfluorooctane sulfonic acid	affects expression	1
tebuconazole	decreases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	affects cotreatment, affects methylation	1
Acetaminophen	decreases expression	1
Estradiol	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Fenofibrate	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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