LRRC53

Summary

LRRC53 (leucine rich repeat containing 53, HGNC:25255) is a protein-coding gene on chromosome 1p31.1, encoding Leucine-rich repeat-containing protein 53 (A6NM62).

Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 105378803 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001382280

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25255
Approved symbol	LRRC53
Name	leucine rich repeat containing 53
Location	1p31.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000162621
Ensembl biotype	protein_coding
Entrez	105378803

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000294635

RefSeq mRNA: 2 — MANE Select: NM_001382280 NM_001364666, NM_001382280

CCDS: CCDS90978

Canonical transcript exons

ENST00000294635 — 5 exons

Exon	Start	End
ENSE00001066981	74469376	74472201
ENSE00001066983	74480153	74480968
ENSE00001184790	74475295	74475810
ENSE00001754424	74512526	74512611
ENSE00001798052	74483262	74483375

Expression profiles

Bgee: expression breadth broad, 26 present calls, max score 72.73.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.73	gold quality
calcaneal tendon	UBERON:0003701	65.30	gold quality
superior frontal gyrus	UBERON:0002661	54.52	gold quality
prefrontal cortex	UBERON:0000451	53.77	gold quality
frontal cortex	UBERON:0001870	50.27	gold quality
Brodmann (1909) area 9	UBERON:0013540	49.27	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	47.60	gold quality
apex of heart	UBERON:0002098	46.88	gold quality
primary visual cortex	UBERON:0002436	46.57	silver quality
cerebral cortex	UBERON:0000956	46.52	gold quality
heart left ventricle	UBERON:0002084	46.49	gold quality
anterior cingulate cortex	UBERON:0009835	46.37	gold quality
colonic epithelium	UBERON:0000397	45.31	gold quality
corpus callosum	UBERON:0002336	44.60	silver quality
right frontal lobe	UBERON:0002810	44.57	gold quality
heart	UBERON:0000948	43.96	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	41.79	gold quality
right atrium auricular region	UBERON:0006631	41.75	gold quality
islet of Langerhans	UBERON:0000006	40.79	silver quality
cortical plate	UBERON:0005343	39.91	gold quality
ventricular zone	UBERON:0003053	39.89	gold quality
skeletal muscle tissue	UBERON:0001134	39.47	gold quality
rectum	UBERON:0001052	39.00	silver quality
muscle tissue	UBERON:0002385	38.76	gold quality
hindlimb stylopod muscle	UBERON:0004252	38.47	gold quality
bone marrow cell	CL:0002092	38.42	gold quality
brain	UBERON:0000955	37.91	gold quality
ganglionic eminence	UBERON:0004023	37.16	gold quality
right hemisphere of cerebellum	UBERON:0014890	35.94	silver quality
Ammon’s horn	UBERON:0001954	35.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.93

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	chadla	ENSDARG00000055160
drosophila_melanogaster	trn	FBGN0010452
drosophila_melanogaster	caps	FBGN0023095
drosophila_melanogaster	CG6749	FBGN0036040
drosophila_melanogaster	CG32055	FBGN0052055
caenorhabditis_elegans		WBGENE00016974

Paralogs (22): IGFALS (ENSG00000099769), TLR8 (ENSG00000101916), LRRC17 (ENSG00000128606), RXFP2 (ENSG00000133105), CD180 (ENSG00000134061), TLR4 (ENSG00000136869), TLR2 (ENSG00000137462), LRRC32 (ENSG00000137507), LRRC3 (ENSG00000160233), TLR3 (ENSG00000164342), VASN (ENSG00000168140), RXFP1 (ENSG00000171509), NRROS (ENSG00000174004), TLR10 (ENSG00000174123), TLR1 (ENSG00000174125), TLR6 (ENSG00000174130), LRRC3B (ENSG00000179796), TSKU (ENSG00000182704), TLR5 (ENSG00000187554), TLR7 (ENSG00000196664), LRIT2 (ENSG00000204033), LRRC3C (ENSG00000204913)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 53 — A6NM62 (reviewed: A6NM62)

All UniProt accessions (1): A6NM62

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (2): NP_001351595, NP_001369209* (*=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
IPR050541	LRR_TM_domain-containing	Family

Pfam: PF13855

UniProt features (15 total): repeat 7, region of interest 3, compositionally biased region 2, chain 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NM62-F1	44.53	0.15

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr1p31

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

254 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC53	SUOX	P51687	102
LRRC53	MOB1A	Q9H8S9	91
LRRC53	RBM25	P49756	90
LRRC53	PPP1R11	O60927	90
LRRC53	SNRPD2	P43330	90
LRRC53	SNRPD3	P43331	89
LRRC53	SF3B3	Q15393	84
LRRC53	XAB2	Q9HCS7	84
LRRC53	LSM8	O95777	81
LRRC53	SNRPE	P08578	80
LRRC53	PRPF39	Q86UA1	80
LRRC53	SF3B1	O75533	79
LRRC53	SART1	O43290	73
LRRC53	RBMX2	Q9Y388	71
LRRC53	NTNG1	Q9Y2I2	70

IntAct

1 interactions, top by confidence:

A	B	Type	Score
	FER1L5	psi-mi:“MI:0915”(physical association)	0.400

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A2AGB2, A2ALV5, A3KMW7, A6NM62, A8MT70, A9JRX0, D3Z987, P15975, P56716, P70347, Q0P5X5, Q0VET5, Q28FY7, Q2M2Z5, Q3MHT3, Q3U0P1, Q3U3V8, Q3UXL4, Q3V089, Q5SXH7, Q5T1N1, Q5T4T6, Q5VXU9, Q68CR7, Q6NZK5, Q6P2D8, Q7M6U3, Q7Z4H7, Q7Z572, Q7ZYI3, Q7ZZH7, Q80VP2, Q86T90, Q86YC2, Q8BG34, Q8BL06, Q8CCC3, Q8MJ03

Diamond homologs: A6NM62, Q9BGY6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1963 predictions. Top by Δscore:

Variant	Effect	Δscore
1:74472202:C:T	acceptor_loss	1.0000
1:74472203:T:G	acceptor_loss	1.0000
1:74483264:A:AC	donor_gain	1.0000
1:74483265:C:CC	donor_gain	1.0000
1:74492153:T:TA	acceptor_gain	1.0000
1:74472199:TAT:T	acceptor_gain	0.9900
1:74472202:C:CC	acceptor_gain	0.9900
1:74477730:T:A	donor_gain	0.9900
1:74492050:A:AG	acceptor_gain	0.9900
1:74492050:ACCT:A	acceptor_gain	0.9900
1:74492051:C:G	acceptor_gain	0.9900
1:74492095:AGCT:A	acceptor_gain	0.9900
1:74492096:GCTG:G	acceptor_gain	0.9900
1:74492161:T:A	acceptor_gain	0.9900
1:74492161:T:TA	acceptor_gain	0.9900
1:74472200:AT:A	acceptor_gain	0.9800
1:74472204:G:C	acceptor_gain	0.9800
1:74472204:G:GC	acceptor_gain	0.9800
1:74477409:TGAGC:T	donor_gain	0.9800
1:74483277:G:C	donor_gain	0.9800
1:74489183:TTACA:T	acceptor_loss	0.9800
1:74489184:TACAG:T	acceptor_loss	0.9800
1:74489185:ACAGG:A	acceptor_loss	0.9800
1:74489186:CAG:C	acceptor_loss	0.9800
1:74489186:CAGGG:C	acceptor_loss	0.9800
1:74489187:A:AT	acceptor_loss	0.9800
1:74489187:A:C	acceptor_loss	0.9800
1:74489187:AG:A	acceptor_gain	0.9800
1:74489188:G:GA	acceptor_loss	0.9800
1:74489188:GG:G	acceptor_gain	0.9800

AlphaMissense

8244 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:74480409:C:A	W216C	0.989
1:74480409:C:G	W216C	0.989
1:74480411:A:G	W216R	0.986
1:74480411:A:T	W216R	0.986
1:74480373:A:C	F228L	0.984
1:74480373:A:T	F228L	0.984
1:74480375:A:G	F228L	0.984
1:74475793:A:G	C308R	0.983
1:74475801:C:T	G305D	0.973
1:74475802:C:G	G305R	0.973
1:74480415:G:C	N214K	0.967
1:74480415:G:T	N214K	0.967
1:74480556:A:C	N167K	0.966
1:74480556:A:T	N167K	0.966
1:74480484:A:C	N191K	0.964
1:74480484:A:T	N191K	0.964
1:74480479:A:G	L193S	0.963
1:74475804:A:T	V304D	0.962
1:74480153:C:G	G302R	0.959
1:74480153:C:T	G302R	0.959
1:74480485:T:A	N191I	0.958
1:74480162:C:G	G299R	0.957
1:74480457:A:C	F200L	0.956
1:74480457:A:T	F200L	0.956
1:74480459:A:G	F200L	0.956
1:74480494:A:G	L188P	0.954
1:74480458:A:G	F200S	0.952
1:74480634:A:C	N141K	0.952
1:74480634:A:T	N141K	0.952
1:74480161:C:T	G299D	0.951

dbSNP variants (sampled 300 via entrez): RS1000009318 (1:74509097 A>G,T), RS1000044157 (1:74532088 C>A), RS1000053256 (1:74493493 A>G,T), RS1000055319 (1:74472470 T>C), RS1000063103 (1:74509482 T>G), RS1000174943 (1:74517585 G>A), RS1000209641 (1:74531360 A>G), RS1000213462 (1:74508833 A>G), RS1000265112 (1:74514401 T>C), RS1000269877 (1:74531910 C>T), RS1000274030 (1:74491657 G>A), RS1000321269 (1:74531677 T>C,G), RS1000343205 (1:74487009 C>T), RS1000384443 (1:74480894 G>A), RS1000415261 (1:74531867 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
Resveratrol	affects cotreatment, decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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