LRRC75A

Summary

LRRC75A (leucine rich repeat containing 75A, HGNC:32403) is a protein-coding gene on chromosome 17p11.2, encoding Leucine-rich repeat-containing protein 75A (Q8NAA5).

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul2-RING ubiquitin ligase complex. Predicted to be active in cytoplasm.

Source: NCBI Gene 388341 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_001113567

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32403
Approved symbol	LRRC75A
Name	leucine rich repeat containing 75A
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35696
Ensembl gene	ENSG00000181350
Ensembl biotype	protein_coding
Entrez	388341

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000409083, ENST00000409887, ENST00000470794, ENST00000934492, ENST00000934493

RefSeq mRNA: 2 — MANE Select: NM_001113567 NM_001113567, NM_207387

CCDS: CCDS11178, CCDS45620

Canonical transcript exons

ENST00000470794 — 4 exons

Exon	Start	End
ENSE00001248103	16462258	16462386
ENSE00001584842	16447845	16447960
ENSE00001889030	16491745	16492193
ENSE00001949860	16441577	16444131

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 91.92.

FANTOM5 (CAGE): breadth broad, TPM avg 1.7024 / max 87.0739, expressed in 686 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164735	0.7277	338
164737	0.5748	351
164732	0.1932	84
164736	0.1191	43
164734	0.0565	18
164733	0.0311	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	91.92	gold quality
jejunal mucosa	UBERON:0000399	89.72	gold quality
mucosa of transverse colon	UBERON:0004991	89.64	gold quality
duodenum	UBERON:0002114	86.24	gold quality
right adrenal gland	UBERON:0001233	82.91	gold quality
rectum	UBERON:0001052	82.86	gold quality
colonic mucosa	UBERON:0000317	82.73	gold quality
right adrenal gland cortex	UBERON:0035827	82.45	gold quality
small intestine Peyer’s patch	UBERON:0003454	82.07	gold quality
small intestine	UBERON:0002108	82.05	gold quality
transverse colon	UBERON:0001157	81.74	gold quality
mucosa of sigmoid colon	UBERON:0004993	81.68	gold quality
left adrenal gland	UBERON:0001234	81.16	gold quality
adrenal gland	UBERON:0002369	80.73	gold quality
ganglionic eminence	UBERON:0004023	80.53	gold quality
left adrenal gland cortex	UBERON:0035825	80.12	gold quality
adrenal cortex	UBERON:0001235	79.83	gold quality
adrenal tissue	UBERON:0018303	79.52	gold quality
cortical plate	UBERON:0005343	79.01	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.56	gold quality
ventricular zone	UBERON:0003053	78.38	gold quality
prefrontal cortex	UBERON:0000451	77.83	gold quality
intestine	UBERON:0000160	77.64	gold quality
large intestine	UBERON:0000059	76.19	gold quality
colon	UBERON:0001155	76.19	gold quality
spleen	UBERON:0002106	75.30	gold quality
anterior cingulate cortex	UBERON:0009835	75.06	gold quality
right frontal lobe	UBERON:0002810	74.88	gold quality
neocortex	UBERON:0001950	74.35	gold quality
frontal cortex	UBERON:0001870	74.15	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-GEOD-76312	yes	9318.03
E-MTAB-9543	yes	3699.29
E-HCAD-6	yes	1229.13
E-MTAB-7008	yes	1220.50
E-MTAB-5061	yes	1101.17
E-HCAD-56	yes	960.63
E-MTAB-10596	yes	494.33
E-MTAB-8559	yes	486.19
E-MTAB-9067	yes	18.14
E-CURD-112	yes	13.58
E-ANND-3	yes	4.49
E-MTAB-4850	no	507.19
E-MTAB-9801	no	4.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

69 targeting LRRC75A, 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-3646	100.00	73.56	5283
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4639-5P	99.81	67.37	1028
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-4478	99.07	65.16	2320

Literature-anchored findings (GeneRIF, showing 1)

• Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia. (PMID:37263619)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrrc75a	ENSDARG00000076834
mus_musculus	Lrrc75a	ENSMUSG00000046417
rattus_norvegicus	Lrrc75a	ENSRNOG00000073513

Protein

Protein identifiers

Leucine-rich repeat-containing protein 75A — Q8NAA5 (reviewed: Q8NAA5)

Alternative names: Leucine-rich repeat-containing protein FAM211A

All UniProt accessions (1): Q8NAA5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the LRRC75 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8NAA5-1	1	yes
Q8NAA5-2	2

RefSeq proteins (2): NP_001107039, NP_997270 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR032675	LRR_dom_sf	Homologous_superfamily

UniProt features (8 total): repeat 2, region of interest 2, splice variant 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NAA5-F1	75.23	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AACTTT_UNKNOWN, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, ATGTCAC_MIR489, GOBP_PROTEIN_CATABOLIC_PROCESS, TGGAAA_NFAT_Q4_01, GOCC_TRANSFERASE_COMPLEX, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOBP_PROTEOLYSIS, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_UBIQUITIN_LIGASE_COMPLEX, MEISSNER_NPC_HCP_WITH_H3K4ME2, MARTENS_TRETINOIN_RESPONSE_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN

GO Biological Process (1): proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (1): ubiquitin-like ligase-substrate adaptor activity (GO:1990756)

GO Cellular Component (2): cytoplasm (GO:0005737), Cul2-RING ubiquitin ligase complex (GO:0031462)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
enzyme-substrate adaptor activity	1
intracellular anatomical structure	1
cellular anatomical structure	1
cullin-RING ubiquitin ligase complex	1

Protein interactions and networks

STRING

184 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC75A	NICOL1	Q5BLP8	359
LRRC75A	SPATS2	Q86XZ4	331
LRRC75A	FBRSL1	Q9HCM7	329
LRRC75A	KLHL35	Q6PF15	329
LRRC75A	KLHDC8B	Q8IXV7	322
LRRC75A	ZNFX1	Q9P2E3	322
LRRC75A	DIP2B	Q9P265	306
LRRC75A	SSBP4	Q9BWG4	305
LRRC75A	SAMD14	Q8IZD0	305
LRRC75A	TLCD4	Q96MV1	293
LRRC75A	DOK6	Q6PKX4	293
LRRC75A	EHBP1L1	Q8N3D4	291
LRRC75A	C1orf122	Q6ZSJ8	271
LRRC75A	SEC14L6	B5MCN3	271
LRRC75A	LRRN2	O75325	270

IntAct

0 interactions, top by confidence:

BioGRID (2): PRCP (Co-fractionation), LRRC75A (Affinity Capture-RNA)

ESM2 similar proteins: A0A1W2PP97, A6NLX4, A6QNY1, P0DJK0, P12838, P13207, P22389, P22749, P23943, P29473, P29474, P55056, P70313, P79209, P97270, P98162, Q1RMT9, Q28969, Q2TAL6, Q2VPJ9, Q4TUC0, Q566C8, Q5BIR3, Q5JTB6, Q5NRP8, Q5RCS3, Q5SPX3, Q5XIX0, Q62600, Q64322, Q7TMJ8, Q7TPD7, Q7TSF4, Q80TT8, Q867D0, Q8BZT7, Q8C8N3, Q8K1T4, Q8K4Z2, Q8MJW9

Diamond homologs: A0A0G2JMD5, A3QJZ6, A3QJZ7, A5PJJ5, A6NGN4, E9Q5G7, H0Y7S4, O60809, O60810, O60811, O60813, O95521, O95522, P0DUQ1, P0DUQ2, P59047, P78395, Q15048, Q3UWY1, Q569B5, Q5SWL7, Q5SWL8, Q5TYX0, Q5VT98, Q5VTA0, Q5VWM3, Q5VWM4, Q5VWM6, Q5VXH4, Q5VXH5, Q7TPX8, Q7TSF4, Q810Y8, Q8NAA5, Q8VC16, Q99MW3, Q2VPJ9, Q7TPD7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	10
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

637 predictions. Top by Δscore:

Variant	Effect	Δscore
17:16462257:CCGG:C	donor_gain	1.0000
17:16462283:G:A	donor_gain	1.0000
17:16462385:TC:T	acceptor_gain	1.0000
17:16462385:TCCTG:T	acceptor_loss	1.0000
17:16462386:CC:C	acceptor_gain	1.0000
17:16462386:CCTG:C	acceptor_loss	1.0000
17:16462387:C:CG	acceptor_loss	1.0000
17:16462388:T:G	acceptor_loss	1.0000
17:16491740:CTCA:C	donor_loss	1.0000
17:16491741:TCAC:T	donor_loss	1.0000
17:16491742:CAC:C	donor_loss	1.0000
17:16491743:A:T	donor_loss	1.0000
17:16491744:CCTGG:C	donor_gain	1.0000
17:16444127:TGAGG:T	acceptor_gain	0.9900
17:16444128:GAGGC:G	acceptor_gain	0.9900
17:16444129:AGG:A	acceptor_gain	0.9900
17:16444129:AGGCT:A	acceptor_gain	0.9900
17:16444130:GG:G	acceptor_gain	0.9900
17:16444130:GGCT:G	acceptor_gain	0.9900
17:16444131:GCTG:G	acceptor_gain	0.9900
17:16444132:C:CC	acceptor_gain	0.9900
17:16444132:CTG:C	acceptor_gain	0.9900
17:16444133:T:G	acceptor_gain	0.9900
17:16447836:GTAAC:G	donor_loss	0.9900
17:16447837:TAACT:T	donor_loss	0.9900
17:16447838:AACT:A	donor_loss	0.9900
17:16447839:ACT:A	donor_loss	0.9900
17:16447840:CTCAC:C	donor_loss	0.9900
17:16447841:TCAC:T	donor_loss	0.9900
17:16447842:CACCA:C	donor_loss	0.9900

AlphaMissense

2190 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:16443810:G:C	N271K	1.000
17:16443810:G:T	N271K	1.000
17:16443813:G:C	N270K	1.000
17:16443813:G:T	N270K	1.000
17:16443907:C:A	G239V	1.000
17:16443990:G:C	F211L	1.000
17:16443990:G:T	F211L	1.000
17:16443992:A:G	F211L	1.000
17:16447917:A:G	L140P	1.000
17:16462298:A:G	L112P	1.000
17:16443730:A:G	I298T	0.999
17:16443814:T:A	N270I	0.999
17:16443820:A:G	L268P	0.999
17:16443830:A:G	W265R	0.999
17:16443830:A:T	W265R	0.999
17:16443898:A:G	L242S	0.999
17:16443903:G:C	N240K	0.999
17:16443903:G:T	N240K	0.999
17:16443907:C:T	G239D	0.999
17:16447905:A:G	L144P	0.999
17:16447907:G:C	H143Q	0.999
17:16447907:G:T	H143Q	0.999
17:16447909:G:C	H143D	0.999
17:16462286:A:G	L116P	0.999
17:16462307:G:A	T109I	0.999
17:16462307:G:C	T109R	0.999
17:16462307:G:T	T109K	0.999
17:16462316:T:A	D106V	0.999
17:16462316:T:C	D106G	0.999
17:16462330:G:C	F101L	0.999

dbSNP variants (sampled 300 via entrez): RS1000110017 (17:16458946 A>G), RS1000128171 (17:16458670 G>A), RS1000181144 (17:16468459 C>T), RS1000252494 (17:16491524 G>C,T), RS1000281348 (17:16471836 G>A), RS1000348007 (17:16464706 C>T), RS1000395544 (17:16476927 A>C,G), RS1000412473 (17:16447766 C>A,T), RS1000428020 (17:16485658 G>C,T), RS1000528865 (17:16480153 C>A,G), RS1000561873 (17:16479870 G>A), RS1000693820 (17:16475289 G>A), RS1000706446 (17:16453018 C>T), RS1000780278 (17:16466964 T>G), RS1000797656 (17:16469804 C>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
GCST007001_11	Cerebrospinal AB1-42 levels in normal cognition	6.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004670	beta-amyloid 1-42 measurement

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
Valproic Acid	affects expression, increases expression	3
Benzo(a)pyrene	affects methylation, increases expression	2
Aflatoxin B1	increases methylation	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
abrine	decreases expression	1
bisphenol S	decreases methylation	1
jinfukang	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Arsenic	affects methylation	1
Cisplatin	decreases expression, affects cotreatment	1
Estradiol	affects cotreatment, decreases expression	1
Lead	affects expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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