LRRC61

Summary

LRRC61 (leucine rich repeat containing 61, HGNC:21704) is a protein-coding gene on chromosome 7q36.1, encoding Leucine-rich repeat-containing protein 61 (Q9BV99).

Predicted to enable alpha-tubulin binding activity and dynein heavy chain binding activity. Predicted to be involved in outer dynein arm assembly. Predicted to be active in cytoplasm.

Source: NCBI Gene 65999 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 73 total
• MANE Select transcript: NM_001142928

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21704
Approved symbol	LRRC61
Name	leucine rich repeat containing 61
Location	7q36.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC3036, FLJ31392, HSPC295
Ensembl gene	ENSG00000127399
Ensembl biotype	protein_coding
Entrez	65999

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000323078, ENST00000359623, ENST00000493307

RefSeq mRNA: 4 — MANE Select: NM_001142928 NM_001142928, NM_001363433, NM_001363434, NM_023942

CCDS: CCDS5901

Canonical transcript exons

ENST00000359623 — 3 exons

Exon	Start	End
ENSE00001402507	150325841	150326010
ENSE00001727313	150336718	150338156
ENSE00001846356	150323355	150323560

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 90.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3007 / max 140.7575, expressed in 1110 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
81922	5.5958	1013
81919	1.6167	315
81921	0.9456	564
81918	0.1112	10
81923	0.0200	9
81924	0.0115	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	90.57	gold quality
cortical plate	UBERON:0005343	88.75	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.43	gold quality
right adrenal gland	UBERON:0001233	86.13	gold quality
right adrenal gland cortex	UBERON:0035827	86.07	gold quality
left adrenal gland	UBERON:0001234	85.50	gold quality
left adrenal gland cortex	UBERON:0035825	85.46	gold quality
adrenal cortex	UBERON:0001235	84.89	gold quality
ganglionic eminence	UBERON:0004023	84.53	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	84.38	gold quality
right lobe of liver	UBERON:0001114	83.97	gold quality
embryo	UBERON:0000922	83.49	gold quality
ventricular zone	UBERON:0003053	83.18	gold quality
epithelium of bronchus	UBERON:0002031	82.61	gold quality
nasal cavity epithelium	UBERON:0005384	82.61	gold quality
bronchus	UBERON:0002185	82.36	gold quality
mucosa of transverse colon	UBERON:0004991	82.33	gold quality
adenohypophysis	UBERON:0002196	82.05	gold quality
adrenal gland	UBERON:0002369	81.98	gold quality
left ovary	UBERON:0002119	81.39	gold quality
bronchial epithelial cell	CL:0002328	80.94	gold quality
right ovary	UBERON:0002118	80.82	gold quality
pituitary gland	UBERON:0000007	80.61	gold quality
thymus	UBERON:0002370	80.55	gold quality
metanephros cortex	UBERON:0010533	80.26	gold quality
hypothalamus	UBERON:0001898	80.21	gold quality
type B pancreatic cell	CL:0000169	79.84	gold quality
gingival epithelium	UBERON:0001949	79.65	gold quality
triceps brachii	UBERON:0001509	79.54	gold quality
liver	UBERON:0002107	79.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GATA3

miRNA regulators (miRDB)

17 targeting LRRC61, 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-3162-3P	100.00	65.37	363
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-7112-5P	99.59	65.76	104
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-3138	98.41	67.53	744
HSA-MIR-147A	98.33	66.40	795
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-6515-5P	97.08	65.48	1219
HSA-MIR-7847-3P	96.63	64.58	952
HSA-MIR-3651	95.62	64.67	287
HSA-MIR-6732-5P	93.97	64.65	422

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc61	ENSDARG00000077357
mus_musculus	Lrrc61	ENSMUSG00000073096
rattus_norvegicus	Lrrc61	ENSRNOG00000008234
drosophila_melanogaster	TbCMF46	FBGN0032163
drosophila_melanogaster	Ppr-Y	FBGN0046697

Paralogs (13): LRRC23 (ENSG00000010626), DNAAF11 (ENSG00000129295), LRRC9 (ENSG00000131951), LRRCC1 (ENSG00000133739), LRRC49 (ENSG00000137821), LRRC46 (ENSG00000141294), DNAAF1 (ENSG00000154099), LRGUK (ENSG00000155530), LRRC43 (ENSG00000158113), LRRIQ3 (ENSG00000162620), DRC3 (ENSG00000171962), PPP1R42 (ENSG00000178125), CEP97 (ENSG00000182504)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 61 — Q9BV99 (reviewed: Q9BV99)

All UniProt accessions (2): Q9BV99, A0A090N7W5

RefSeq proteins (4): NP_001136400, NP_001350362, NP_001350363, NP_076431 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily

Pfam: PF13855

UniProt features (7 total): repeat 4, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BV99-F1	84.67	0.62

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN, LIU_SMARCA4_TARGETS, MODULE_342, EPPERT_LSC_R, HATADA_METHYLATED_IN_LUNG_CANCER_UP, PASTURAL_RIZ1_TARGETS_UP, KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3, DELACROIX_RAR_BOUND_ES, KRIEG_HYPOXIA_NOT_VIA_KDM3A, MYC_UP.V1_UP, PRC2_EZH2_UP.V1_DN, PRC2_SUZ12_UP.V1_DN, KRAS.DF.V1_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_DN, GSE14415_INDUCED_TREG_VS_TCONV_DN

GO Biological Process (1): outer dynein arm assembly (GO:0036158)

GO Molecular Function (3): alpha-tubulin binding (GO:0043014), dynein heavy chain binding (GO:0045504), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
axonemal dynein complex assembly	1
tubulin binding	1
protein binding	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

837 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC61	ZBED10P	Q96FA7	715
LRRC61	KRABD3	A5PL33	613
LRRC61	ACTR3C	Q9C0K3	584
LRRC61	GPR12	P47775	528
LRRC61	WASHC3	Q9Y3C0	499
LRRC61	C7orf33	Q8WU49	479
LRRC61	ZNF584	Q8IVC4	479
LRRC61	DRC11L	A6NCM1	476
LRRC61	SCML4	Q8N228	475
LRRC61	HEATR4	Q86WZ0	447
LRRC61	A0A087WTJ2	A0A087WTJ2	434
LRRC61	TMEM150B	A6NC51	432
LRRC61	ATP6V0E2	Q8NHE4	430
LRRC61	MACROD2	A1Z1Q3	427
LRRC61	ZNF425	Q6IV72	419

IntAct

48 interactions, top by confidence:

A	B	Type	Score
HGS	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
FAM222B	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
LRRC61	ENKD1	psi-mi:“MI:0915”(physical association)	0.560
PKN1	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
EFHC1	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
C1orf216	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
LRRC61	LSAMP	psi-mi:“MI:0915”(physical association)	0.560
NDUFS1	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
LRRC61	ICAM5	psi-mi:“MI:0915”(physical association)	0.560
DNALI1	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
BAG6	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
KLF11	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
NUP58	LRRC61	psi-mi:“MI:0915”(physical association)	0.560
COL26A1	LRRC61	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (46): LRRC61 (Affinity Capture-RNA), LRRC61 (Affinity Capture-RNA), LRRC61 (Two-hybrid), LRRC61 (Two-hybrid), LRRC61 (Two-hybrid), C1orf216 (Two-hybrid), FAM222B (Two-hybrid), HGS (Two-hybrid), YME1L1 (Affinity Capture-MS), NDUFAF4 (Affinity Capture-MS), TEX264 (Affinity Capture-MS), SLC3A2 (Affinity Capture-MS), CUX1 (Affinity Capture-MS), LRRC61 (Proximity Label-MS), FKBP8 (Proximity Label-MS)

ESM2 similar proteins: A4FV98, A5D7B1, A5PK51, A6QLN9, A8MUP2, D3ZVU9, O15527, O35595, O75078, O95848, P57775, Q05B60, Q06643, Q14728, Q14CX5, Q1LZB9, Q27HK4, Q2T9T5, Q2TBS1, Q3UGX3, Q4R3I0, Q4V892, Q58CT4, Q5E9H2, Q5RCI5, Q5SUV1, Q5TM22, Q642A6, Q6IA17, Q6PCB0, Q6XQN6, Q862Z7, Q8N8L6, Q8R2R5, Q8R2Z5, Q8R366, Q8WUG5, Q95JH0, Q95JH2, Q969P0

Diamond homologs: Q2T9T5, Q8R2R5, Q9BV99

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

601 predictions. Top by Δscore:

Variant	Effect	Δscore
7:150323558:CAGG:C	donor_loss	1.0000
7:150323559:AGG:A	donor_loss	1.0000
7:150323560:GGT:G	donor_loss	1.0000
7:150323562:T:A	donor_loss	1.0000
7:150328744:T:G	donor_gain	1.0000
7:150323561:G:GG	donor_gain	0.9900
7:150326006:CTAAG:C	donor_loss	0.9900
7:150326007:TAAG:T	donor_loss	0.9900
7:150326008:AAGG:A	donor_loss	0.9900
7:150326009:AG:A	donor_loss	0.9900
7:150326010:GG:G	donor_loss	0.9900
7:150326011:G:GC	donor_loss	0.9900
7:150326012:T:C	donor_loss	0.9900
7:150323556:CTCAG:C	donor_gain	0.9800
7:150323559:AG:A	donor_gain	0.9800
7:150323560:GG:G	donor_gain	0.9800
7:150323557:TCAG:T	donor_gain	0.9700
7:150323558:CAG:C	donor_gain	0.9700
7:150325839:A:AG	acceptor_gain	0.9700
7:150325840:G:GG	acceptor_gain	0.9700
7:150325840:GATTC:G	acceptor_gain	0.9700
7:150328743:GT:G	donor_gain	0.9600
7:150328744:TT:T	donor_gain	0.9600
7:150325833:C:G	acceptor_gain	0.9400
7:150325837:TTAG:T	acceptor_loss	0.9400
7:150325838:TA:T	acceptor_loss	0.9400
7:150325839:A:C	acceptor_loss	0.9400
7:150336712:CCTCA:C	acceptor_loss	0.9400
7:150336713:CTCAG:C	acceptor_loss	0.9400
7:150336714:TCAG:T	acceptor_loss	0.9400

AlphaMissense

1626 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:150337100:T:A	L80H	0.987
7:150337106:T:A	V82D	0.986
7:150337182:C:A	N107K	0.986
7:150337182:C:G	N107K	0.986
7:150336943:T:C	F28L	0.985
7:150336945:C:A	F28L	0.985
7:150336945:C:G	F28L	0.985
7:150337157:T:C	L99S	0.979
7:150337100:T:C	L80P	0.978
7:150337275:C:A	N138K	0.978
7:150337275:C:G	N138K	0.978
7:150337034:T:C	L58P	0.977
7:150337116:T:A	N85K	0.976
7:150337116:T:G	N85K	0.976
7:150337166:T:C	L102P	0.975
7:150337166:T:A	L102H	0.974
7:150337040:T:C	L60P	0.972
7:150337181:A:T	N107I	0.963
7:150337040:T:A	L60Q	0.961
7:150337034:T:A	L58Q	0.959
7:150337100:T:G	L80R	0.959
7:150337034:T:G	L58R	0.958
7:150337040:T:G	L60R	0.957
7:150337050:C:A	N63K	0.956
7:150337050:C:G	N63K	0.956
7:150337172:C:A	A104D	0.955
7:150336927:G:C	K22N	0.954
7:150336927:G:T	K22N	0.954
7:150337015:T:C	C52R	0.953
7:150337343:A:T	D161V	0.952

dbSNP variants (sampled 300 via entrez): RS1000063409 (7:150324086 G>T), RS1000076312 (7:150330182 C>T), RS1000325369 (7:150335247 T>C), RS1000415450 (7:150324190 G>A), RS1000557839 (7:150333397 C>T), RS1000597614 (7:150327806 C>G), RS1000843393 (7:150318490 G>A), RS1001122857 (7:150316616 G>C), RS1001181158 (7:150333082 G>T), RS1001358714 (7:150308811 T>C), RS1001423706 (7:150310445 C>G), RS1001444081 (7:150308421 C>T), RS1001529068 (7:150328858 G>A), RS1001693033 (7:150322903 T>C), RS1001749736 (7:150329086 G>A,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

1 associations (top):

Study	Trait	p-value
GCST004735_5	Epstein-Barr virus copy number in lymphoblastoid cell lines	4.000000e-06

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
Air Pollutants	increases abundance, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
pirinixic acid	affects binding, decreases expression, increases activity	1
sodium arsenite	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Mercuric Chloride	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Vanadates	decreases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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