LRRC71

Summary

LRRC71 (leucine rich repeat containing 71, HGNC:26556) is a protein-coding gene on chromosome 1q23.1, encoding Leucine-rich repeat-containing protein 71 (Q8N4P6).

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 89 total
• MANE Select transcript: NM_144702

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26556
Approved symbol	LRRC71
Name	leucine rich repeat containing 71
Location	1q23.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32884
Ensembl gene	ENSG00000160838
Ensembl biotype	protein_coding
Entrez	149499

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000337428, ENST00000472465, ENST00000476550, ENST00000490146, ENST00000883915, ENST00000883916

RefSeq mRNA: 1 — MANE Select: NM_144702 NM_144702

CCDS: CCDS44249

Canonical transcript exons

ENST00000337428 — 15 exons

Exon	Start	End
ENSE00001257115	156931916	156932027
ENSE00001257153	156927202	156927270
ENSE00001363136	156932424	156932545
ENSE00001446535	156920632	156920963
ENSE00001867412	156932853	156933094
ENSE00003517578	156929636	156929729
ENSE00003521172	156924643	156924718
ENSE00003548140	156927915	156928004
ENSE00003573275	156927733	156927816
ENSE00003590553	156930529	156930617
ENSE00003609687	156924424	156924552
ENSE00003621298	156927496	156927655
ENSE00003628910	156924938	156925015
ENSE00003685261	156929280	156929429
ENSE00003687900	156923949	156924098

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 98.27.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1468 / max 33.3803, expressed in 42 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5794	0.1468	42

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	98.27	gold quality
left testis	UBERON:0004533	91.10	gold quality
bronchial epithelial cell	CL:0002328	90.92	gold quality
right testis	UBERON:0004534	90.72	gold quality
bronchus	UBERON:0002185	89.63	gold quality
testis	UBERON:0000473	87.82	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.24	gold quality
oviduct epithelium	UBERON:0004804	85.16	gold quality
sperm	CL:0000019	82.93	gold quality
kidney epithelium	UBERON:0004819	80.56	gold quality
fallopian tube	UBERON:0003889	80.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.61	gold quality
heart right ventricle	UBERON:0002080	79.21	gold quality
mucosa of paranasal sinus	UBERON:0005030	78.13	gold quality
upper arm skin	UBERON:0004263	76.12	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	74.31	gold quality
right lung	UBERON:0002167	73.68	gold quality
nasal cavity mucosa	UBERON:0001826	70.81	gold quality
myocardium	UBERON:0002349	70.53	gold quality
epithelial cell of pancreas	CL:0000083	70.08	gold quality
left uterine tube	UBERON:0001303	69.85	gold quality
cerebellar vermis	UBERON:0004720	69.60	gold quality
parotid gland	UBERON:0001831	68.90	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	68.19	gold quality
left ventricle myocardium	UBERON:0006566	66.78	gold quality
upper lobe of left lung	UBERON:0008952	66.51	gold quality
quadriceps femoris	UBERON:0001377	66.01	gold quality
adult organism	UBERON:0007023	65.80	gold quality
cardiac muscle of right atrium	UBERON:0003379	65.58	gold quality
vastus lateralis	UBERON:0001379	65.38	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

4 targeting LRRC71, 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-361-3P	99.19	66.45	1381
HSA-MIR-499B-5P	98.35	68.39	988
HSA-MIR-3137	97.26	66.78	761
HSA-MIR-6866-5P	96.64	68.06	624

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc71	ENSDARG00000036412
mus_musculus	Lrrc71	ENSMUSG00000023084
rattus_norvegicus	Lrrc71	ENSRNOG00000014937

Protein

Protein identifiers

Leucine-rich repeat-containing protein 71 — Q8N4P6 (reviewed: Q8N4P6)

All UniProt accessions (1): Q8N4P6

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N4P6-1	1	yes
Q8N4P6-2	2

RefSeq proteins (1): NP_653303* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR053040	LRR-containing_protein_71	Family

Pfam: PF13516

UniProt features (18 total): repeat 5, compositionally biased region 4, splice variant 3, sequence variant 3, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4P6-F1	72.25	0.52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 40 (showing top): BENPORATH_ES_WITH_H3K27ME3, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, HATADA_METHYLATED_IN_LUNG_CANCER_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, FOXJ2_TARGET_GENES, SKIL_TARGET_GENES, ZNF165_TARGET_GENES, ZNF223_TARGET_GENES, ZNF563_TARGET_GENES, ZNF7_TARGET_GENES, ZNF8_TARGET_GENES, GSE13229_IMM_VS_MATURE_NKCELL_DN, GSE13306_RA_VS_UNTREATED_TREG_DN

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

413 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC71	ETV3L	Q6ZN32	596
LRRC71	ANHX	E9PGG2	567
LRRC71	ANKUB1	A6NFN9	561
LRRC71	PEAR1	Q5VY43	540
LRRC71	ANKRD66	B4E2M5	490
LRRC71	FAM216B	Q8N7L0	490
LRRC71	KNDC1	Q76NI1	480
LRRC71	LYPD6B	Q8NI32	469
LRRC71	SLC71A2	Q5SR56	463
LRRC71	DYNLT5	Q8N7M0	455
LRRC71	ARHGEF11	O15085	427
LRRC71	HOATZ	Q6PI97	414
LRRC71	LSM14B	Q9BX40	413
LRRC71	NTRK1	P04629	404
LRRC71	DAW1	Q8N136	403

IntAct

3 interactions, top by confidence:

A	B	Type	Score
LRRC71	PDCD11	psi-mi:“MI:0915”(physical association)	0.400
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): LRRC71 (Proximity Label-MS), LRRC71 (Affinity Capture-MS), LRRC71 (Affinity Capture-MS), LRRC71 (Cross-Linking-MS (XL-MS)), CANX (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A2VD13, A6QP29, A7E3N7, B5DFG1, O75127, P54098, P54099, Q05AA6, Q13474, Q3SX05, Q3SZK4, Q3TYG6, Q3U0L2, Q3U5Q7, Q3URY6, Q3ZBK7, Q4R5Q4, Q53GS7, Q58CQ5, Q5R655, Q5RAS2, Q66H85, Q6NUQ4, Q6ZUX3, Q7YS91, Q80UU1, Q8BKF1, Q8BL74, Q8C0R7, Q8C1F5, Q8C2E4, Q8CJ00, Q8N4P6, Q8R322, Q8TE82, Q969Z0, Q96KN7, Q96MK2, Q99MQ3, Q9BQ95

Diamond homologs: Q8N4P6, Q9D3W5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3198 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156923947:A:AG	acceptor_gain	1.0000
1:156923948:G:GG	acceptor_gain	1.0000
1:156923948:GA:G	acceptor_gain	1.0000
1:156923948:GAGGA:G	acceptor_gain	1.0000
1:156924096:TAGG:T	donor_loss	1.0000
1:156924097:AGGT:A	donor_loss	1.0000
1:156924098:GGT:G	donor_loss	1.0000
1:156924099:G:C	donor_loss	1.0000
1:156924100:T:G	donor_loss	1.0000
1:156924550:GCG:G	donor_gain	1.0000
1:156924552:GGTG:G	donor_loss	1.0000
1:156924553:GT:G	donor_loss	1.0000
1:156924554:T:G	donor_loss	1.0000
1:156924719:G:GG	donor_gain	1.0000
1:156924926:C:A	acceptor_gain	1.0000
1:156927484:C:A	acceptor_gain	1.0000
1:156927515:C:CA	acceptor_gain	1.0000
1:156927516:G:A	acceptor_gain	1.0000
1:156927642:GC:G	donor_gain	1.0000
1:156927651:CGGAC:C	donor_gain	1.0000
1:156927652:GGAC:G	donor_gain	1.0000
1:156927652:GGACG:G	donor_gain	1.0000
1:156927653:G:GT	donor_gain	1.0000
1:156927653:GAC:G	donor_gain	1.0000
1:156927654:AC:A	donor_gain	1.0000
1:156927654:ACG:A	donor_loss	1.0000
1:156927655:CGTG:C	donor_loss	1.0000
1:156927656:G:GG	donor_gain	1.0000
1:156927656:GTGA:G	donor_loss	1.0000
1:156927657:T:A	donor_loss	1.0000

AlphaMissense

3613 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:156924645:T:A	W148R	0.998
1:156924645:T:C	W148R	0.998
1:156927223:C:A	N205K	0.997
1:156927223:C:G	N205K	0.997
1:156927513:T:C	L227P	0.997
1:156927523:T:A	N230K	0.997
1:156927523:T:G	N230K	0.997
1:156927619:C:A	N262K	0.997
1:156927619:C:G	N262K	0.997
1:156924496:T:A	I128N	0.996
1:156932016:T:C	L477P	0.996
1:156932858:T:A	N523K	0.996
1:156932858:T:G	N523K	0.996
1:156923985:T:C	F66S	0.995
1:156927213:T:C	L202P	0.995
1:156927603:T:C	L257P	0.995
1:156927780:C:A	N290K	0.995
1:156927780:C:G	N290K	0.995
1:156927958:G:C	R317P	0.995
1:156932022:T:C	L479P	0.995
1:156932428:C:A	N482K	0.995
1:156932428:C:G	N482K	0.995
1:156923996:T:C	C70R	0.994
1:156924030:T:A	V81D	0.994
1:156927509:T:C	S226P	0.994
1:156927513:T:A	L227Q	0.994
1:156927513:T:G	L227R	0.994
1:156927516:G:C	R228P	0.994
1:156927609:T:C	L259P	0.994
1:156927764:T:C	L285P	0.994

dbSNP variants (sampled 300 via entrez): RS1000005794 (1:156924320 C>A,G), RS1000129944 (1:156923944 C>G,T), RS1000142788 (1:156924001 G>A,C), RS1000294787 (1:156930103 T>TC,TG), RS1000356562 (1:156930030 C>T), RS1000569045 (1:156930537 A>C), RS1000743351 (1:156935173 T>C), RS1000903557 (1:156921922 T>C,G), RS1000976238 (1:156928849 G>T), RS1001703701 (1:156924279 G>C), RS1001798140 (1:156928926 G>A), RS1001943261 (1:156935861 G>A,C,T), RS1002171957 (1:156933444 AT>A), RS1002307714 (1:156933118 G>C,T), RS1002462447 (1:156931833 T>C,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

10 associations (top):

Study	Trait	p-value
GCST010697_36	Cortical surface area (min-P)	5.000000e-08
GCST010698_82	Subcortical volume (min-P)	4.000000e-20
GCST010699_62	Brain morphology (min-P)	2.000000e-26
GCST010700_48	Cortical thickness (MOSTest)	2.000000e-10
GCST010701_53	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_160	Subcortical volume (MOSTest)	1.000000e-21
GCST010703_149	Brain morphology (MOSTest)	2.000000e-09
GCST90000025_772	Appendicular lean mass	4.000000e-12
GCST90002401_362	Platelet distribution width	4.000000e-11
GCST90002403_24	Red blood cell count	5.000000e-13

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0004980	appendicular lean mass
EFO:0007984	platelet component distribution width
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	2
Benzo(a)pyrene	affects methylation	2
Smoke	decreases expression, increases abundance, increases expression	2
glycidyl methacrylate	decreases expression	1
butyraldehyde	increases expression	1
hydroquinone	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Atrazine	increases expression	1
Copper	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Silicon Dioxide	increases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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