LRRC73

Summary

LRRC73 (leucine rich repeat containing 73, HGNC:21375) is a protein-coding gene on chromosome 6p21.1, encoding Leucine-rich repeat-containing protein 73 (Q5JTD7).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_001012974

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21375
Approved symbol	LRRC73
Name	leucine rich repeat containing 73
Location	6p21.1
Locus type	gene with protein product
Status	Approved
Aliases	dJ337H4.2
Ensembl gene	ENSG00000204052
Ensembl biotype	protein_coding
Entrez	221424

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000372441, ENST00000899667

RefSeq mRNA: 2 — MANE Select: NM_001012974 NM_001012974, NM_001271882

CCDS: CCDS34456

Canonical transcript exons

ENST00000372441 — 6 exons

Exon	Start	End
ENSE00001457804	43507456	43507678
ENSE00001457808	43508298	43508420
ENSE00001457809	43508760	43508920
ENSE00003421486	43507826	43507926
ENSE00003978291	43506968	43507308
ENSE00003978292	43509514	43510346

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 89.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5392 / max 240.8794, expressed in 1031 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73690	3.3143	883
73689	0.4975	221
73688	0.4829	200
73686	0.0973	32
73692	0.0567	37
73687	0.0459	11
73691	0.0446	22

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	89.76	gold quality
right testis	UBERON:0004534	89.56	gold quality
testis	UBERON:0000473	86.72	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.59	gold quality
bronchial epithelial cell	CL:0002328	83.56	gold quality
bronchus	UBERON:0002185	82.53	gold quality
prefrontal cortex	UBERON:0000451	81.31	gold quality
right frontal lobe	UBERON:0002810	79.69	gold quality
frontal cortex	UBERON:0001870	79.16	gold quality
neocortex	UBERON:0001950	78.27	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.74	gold quality
nucleus accumbens	UBERON:0001882	77.63	gold quality
anterior cingulate cortex	UBERON:0009835	77.61	gold quality
right adrenal gland cortex	UBERON:0035827	77.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.24	gold quality
right uterine tube	UBERON:0001302	77.16	gold quality
right adrenal gland	UBERON:0001233	76.68	gold quality
cerebral cortex	UBERON:0000956	76.59	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	75.53	gold quality
cortical plate	UBERON:0005343	75.35	gold quality
left adrenal gland	UBERON:0001234	74.97	gold quality
left adrenal gland cortex	UBERON:0035825	74.89	gold quality
adult organism	UBERON:0007023	74.79	gold quality
superior frontal gyrus	UBERON:0002661	74.77	gold quality
forebrain	UBERON:0001890	74.60	gold quality
adrenal cortex	UBERON:0001235	74.40	gold quality
caudate nucleus	UBERON:0001873	74.30	gold quality
amygdala	UBERON:0001876	74.09	gold quality
Ammon’s horn	UBERON:0001954	73.77	gold quality
putamen	UBERON:0001874	73.68	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

miRNA regulators (miRDB)

15 targeting LRRC73, 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-4668-3P	100.00	68.74	2635
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-4725-5P	98.67	65.42	628
HSA-MIR-504-5P	98.67	65.40	631
HSA-MIR-1301-3P	98.64	68.27	1071
HSA-MIR-5047	98.64	68.62	1035
HSA-MIR-7156-3P	98.25	67.66	859
HSA-MIR-376C-3P	97.63	68.88	1263
HSA-MIR-558	97.50	67.16	977
HSA-MIR-1225-3P	97.29	64.60	876
HSA-MIR-6858-3P	96.37	64.41	771
HSA-MIR-1298-3P	94.05	64.84	620
HSA-MIR-615-3P	90.62	68.07	69

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc73	ENSDARG00000063411
mus_musculus	Lrrc73	ENSMUSG00000071073
rattus_norvegicus	Lrrc73	ENSRNOG00000039856

Protein

Protein identifiers

Leucine-rich repeat-containing protein 73 — Q5JTD7 (reviewed: Q5JTD7)

All UniProt accessions (1): Q5JTD7

RefSeq proteins (2): NP_001012992, NP_001258811 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR052201	LRR-containing_regulator	Family

UniProt features (11 total): repeat 7, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JTD7-F1	84.29	0.76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, MIR558, MIR22_3P, MIR7156_3P, GAO_LARGE_INTESTINE_ADULT_CE_OLFM4HIGH_STEM_CELL, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_EYE_GANGLION_CELLS, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_STOMACH_CILIATED_EPITHELIAL_CELLS, FXR1_TARGET_GENES, ZNF140_TARGET_GENES, TRAVAGLINI_LUNG_CILIATED_CELL, TRAVAGLINI_LUNG_PROXIMAL_CILIATED_CELL, GSE20366_EX_VIVO_VS_DEC205_CONVERSION_NAIVE_CD4_TCELL_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

318 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC73	ANKRD13D	Q6ZTN6	665
LRRC73	TEPSIN	Q96N21	626
LRRC73	VSIG10	Q8N0Z9	556
LRRC73	DOCK3	Q8IZD9	510
LRRC73	NPRL2	Q8WTW4	505
LRRC73	POLR3H	Q9Y535	468
LRRC73	FAM153B	P0C7A2	376
LRRC73	ELFN1	P0C7U0	348
LRRC73	BBLN	Q9BUW7	347
LRRC73	ANGPT4	Q9Y264	345
LRRC73	OR4C46	A6NHA9	336
LRRC73	GDF7	Q7Z4P5	334
LRRC73	NCEH1	Q6PIU2	318
LRRC73	JPH3	Q8WXH2	302
LRRC73	MARK2	Q7KZI7	302

IntAct

33 interactions, top by confidence:

A	B	Type	Score
CRTC3	YWHAH	psi-mi:“MI:0914”(association)	0.710
LRRC73	TSHZ3	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	ZNF574	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	NTAQ1	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	ENPP7	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	PICK1	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	RPP25	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	LNX1	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	GADD45GIP1	psi-mi:“MI:0915”(physical association)	0.560
LRRC73	CTDSP1	psi-mi:“MI:0915”(physical association)	0.370
LRRC73	SHANK3	psi-mi:“MI:0915”(physical association)	0.370
LRRC73	THAP12	psi-mi:“MI:0914”(association)	0.350
OR10A4	LRRC73	psi-mi:“MI:0914”(association)	0.350
LRRC73	SLC27A2	psi-mi:“MI:0914”(association)	0.350
LRRC73	DNAJC13	psi-mi:“MI:0914”(association)	0.350
TSHZ3	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
ZNF574	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
GADD45GIP1	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
LNX1	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
NTAQ1	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
ENPP7	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
PICK1	LRRC73	psi-mi:“MI:0915”(physical association)	0.000
RPP25	LRRC73	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (34): LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), LRRC73 (Affinity Capture-MS), LRRC73 (Affinity Capture-MS), LRRC73 (Two-hybrid), LRRC73 (Two-hybrid), TBC1D5 (Affinity Capture-MS), CYHR1 (Affinity Capture-MS), VPS26A (Affinity Capture-MS)

ESM2 similar proteins: A2VDH3, A5A779, A6NIK2, B5X441, D3ZUM2, D4ABB4, E1BNS0, E2RKN7, E6ZHJ8, E9Q7T7, G1T469, I3L5V6, O75325, Q08602, Q08DG4, Q13641, Q3UGP9, Q4R588, Q4R8Y9, Q50LG9, Q53B87, Q53B88, Q587K4, Q5EA80, Q5EBP3, Q5JTD7, Q5NVK5, Q5PQP9, Q5PQV5, Q5VT99, Q6E804, Q6NUI6, Q6NW95, Q6PDS3, Q6SZW1, Q8CIG9, Q8K3Z0, Q8VHS5, Q8WXI3, Q91W61

Diamond homologs: Q587K4, Q5JTD7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

819 predictions. Top by Δscore:

Variant	Effect	Δscore
6:43507455:CCG:C	donor_gain	1.0000
6:43507551:T:TA	donor_gain	1.0000
6:43507674:AGGGT:A	acceptor_gain	1.0000
6:43507675:GGGT:G	acceptor_gain	1.0000
6:43507676:GGT:G	acceptor_gain	1.0000
6:43507677:GT:G	acceptor_gain	1.0000
6:43507678:TCT:T	acceptor_loss	1.0000
6:43507679:C:CC	acceptor_gain	1.0000
6:43507684:G:C	acceptor_gain	1.0000
6:43507684:G:GC	acceptor_gain	1.0000
6:43507694:A:AC	acceptor_gain	1.0000
6:43507694:A:C	acceptor_gain	1.0000
6:43507696:A:AC	acceptor_gain	1.0000
6:43507696:A:C	acceptor_gain	1.0000
6:43507821:C:A	donor_gain	1.0000
6:43508432:C:CT	acceptor_gain	1.0000
6:43508755:CTCA:C	donor_loss	1.0000
6:43508756:TCACC:T	donor_loss	1.0000
6:43508757:CACCA:C	donor_loss	1.0000
6:43508758:A:AC	donor_gain	1.0000
6:43508758:A:AG	donor_loss	1.0000
6:43508759:C:CC	donor_gain	1.0000
6:43508759:CCAG:C	donor_gain	1.0000
6:43508759:CCAGA:C	donor_gain	1.0000
6:43508916:GCAGG:G	acceptor_gain	1.0000
6:43508917:CAGG:C	acceptor_gain	1.0000
6:43508917:CAGGC:C	acceptor_gain	1.0000
6:43508918:AGG:A	acceptor_gain	1.0000
6:43508919:GG:G	acceptor_gain	1.0000
6:43508920:GC:G	acceptor_loss	1.0000

AlphaMissense

2028 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:43507616:G:C	N240K	1.000
6:43507616:G:T	N240K	1.000
6:43507830:G:T	A218D	1.000
6:43508305:G:C	N183K	1.000
6:43508305:G:T	N183K	1.000
6:43508312:T:A	D181V	1.000
6:43508315:A:G	L180P	1.000
6:43508321:A:G	L178P	1.000
6:43508370:A:G	W162R	1.000
6:43508370:A:T	W162R	1.000
6:43508392:G:C	N154K	1.000
6:43508392:G:T	N154K	1.000
6:43508408:A:G	L149P	1.000
6:43508831:C:A	G121V	1.000
6:43508832:C:A	G121W	1.000
6:43509604:A:G	L61P	1.000
6:43507587:A:C	I250S	0.999
6:43507587:A:G	I250T	0.999
6:43507587:A:T	I250N	0.999
6:43507617:T:A	N240I	0.999
6:43507626:A:G	L237S	0.999
6:43507632:A:G	L235P	0.999
6:43507674:A:G	L221P	0.999
6:43507860:A:G	L208S	0.999
6:43507866:A:G	L206P	0.999
6:43507883:A:C	S200R	0.999
6:43507883:A:T	S200R	0.999
6:43507885:T:G	S200R	0.999
6:43507890:G:T	A198D	0.999
6:43507896:G:T	A196D	0.999

dbSNP variants (sampled 300 via entrez): RS1000546252 (6:43509780 C>A,T), RS1001165297 (6:43510432 G>C,T), RS1002296891 (6:43506731 C>CA), RS1004994320 (6:43512065 G>A), RS1005557145 (6:43509279 G>A,C), RS1005702317 (6:43511326 G>A), RS1005964605 (6:43507475 G>A), RS1006600884 (6:43506953 C>T), RS1007304669 (6:43511560 C>T), RS1007737974 (6:43508087 G>T), RS1008002742 (6:43510922 T>A,C), RS1008409957 (6:43510750 A>T), RS1009038693 (6:43508935 G>C,T), RS1009582627 (6:43510991 C>T), RS1009798995 (6:43511193 G>A)

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

4 associations (top):

Study	Trait	p-value
GCST005956_58	Waist-to-hip ratio adjusted for BMI	7.000000e-26
GCST005957_1	Waist-to-hip ratio adjusted for BMI (age <50)	2.000000e-14
GCST005958_2	Waist-to-hip ratio adjusted for BMI (age >50)	2.000000e-19
GCST005962_2	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	3.000000e-31

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	decreases expression, increases abundance, increases expression	2
Valproic Acid	increases methylation, affects expression	2
Aflatoxin B1	increases expression	2
bisphenol A	increases methylation, affects cotreatment	1
sulforaphane	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
N-Nitrosopyrrolidine	increases expression	1
Niclosamide	increases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	increases expression	1
Lactic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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