LRIT2

Summary

LRIT2 (leucine rich repeat, Ig-like and transmembrane domains 2, HGNC:23443) is a protein-coding gene on chromosome 10q23.1, encoding Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2 (A6NDA9).

Predicted to be located in membrane.

Source: NCBI Gene 340745 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 107 total
• MANE Select transcript: NM_001017924

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23443
Approved symbol	LRIT2
Name	leucine rich repeat, Ig-like and transmembrane domains 2
Location	10q23.1
Locus type	gene with protein product
Status	Approved
Aliases	AC022389.4
Ensembl gene	ENSG00000204033
Ensembl biotype	protein_coding
Entrez	340745

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000372113, ENST00000538192

RefSeq mRNA: 2 — MANE Select: NM_001017924 NM_001017924, NM_001284223

CCDS: CCDS31234, CCDS60581

Canonical transcript exons

ENST00000372113 — 3 exons

Exon	Start	End
ENSE00001456935	84224333	84225114
ENSE00001456936	84225411	84225544
ENSE00003896314	84220571	84222680

Expression profiles

Bgee: expression breadth broad, 52 present calls, max score 70.84.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0294 / max 23.6438, expressed in 6 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
110383	0.0214	6
110382	0.0080	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	70.84	gold quality
skin of abdomen	UBERON:0001416	65.81	gold quality
zone of skin	UBERON:0000014	65.31	gold quality
skin of leg	UBERON:0001511	65.06	gold quality
rectum	UBERON:0001052	61.24	gold quality
nucleus accumbens	UBERON:0001882	59.44	gold quality
putamen	UBERON:0001874	59.00	gold quality
caudate nucleus	UBERON:0001873	58.77	gold quality
ganglionic eminence	UBERON:0004023	58.35	gold quality
transverse colon	UBERON:0001157	57.05	gold quality
prefrontal cortex	UBERON:0000451	51.44	gold quality
lower esophagus mucosa	UBERON:0035834	51.38	gold quality
frontal cortex	UBERON:0001870	48.82	gold quality
superior frontal gyrus	UBERON:0002661	48.31	gold quality
Brodmann (1909) area 9	UBERON:0013540	48.22	gold quality
anterior cingulate cortex	UBERON:0009835	48.13	gold quality
ventricular zone	UBERON:0003053	47.74	silver quality
cortical plate	UBERON:0005343	47.69	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	47.52	gold quality
cerebral cortex	UBERON:0000956	47.42	gold quality
small intestine Peyer’s patch	UBERON:0003454	47.12	gold quality
brain	UBERON:0000955	46.61	gold quality
colonic epithelium	UBERON:0000397	46.22	gold quality
small intestine	UBERON:0002108	45.56	gold quality
esophagus mucosa	UBERON:0002469	45.54	gold quality
colon	UBERON:0001155	45.28	gold quality
intestine	UBERON:0000160	45.09	gold quality
primary visual cortex	UBERON:0002436	44.89	silver quality
right frontal lobe	UBERON:0002810	44.81	gold quality
hypothalamus	UBERON:0001898	43.74	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

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

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

61 targeting LRIT2, 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-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-29B-2-5P	99.67	68.98	1726
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-365A-3P	99.43	70.02	836

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lrit2	ENSDARG00000030626
mus_musculus	Lrit2	ENSMUSG00000043418
rattus_norvegicus	Lrit2	ENSRNOG00000022726

Paralogs (22): IGFALS (ENSG00000099769), TLR8 (ENSG00000101916), LRRC17 (ENSG00000128606), RXFP2 (ENSG00000133105), CD180 (ENSG00000134061), TLR4 (ENSG00000136869), TLR2 (ENSG00000137462), LRRC32 (ENSG00000137507), LRRC3 (ENSG00000160233), LRRC53 (ENSG00000162621), TLR3 (ENSG00000164342), VASN (ENSG00000168140), RXFP1 (ENSG00000171509), NRROS (ENSG00000174004), TLR10 (ENSG00000174123), TLR1 (ENSG00000174125), TLR6 (ENSG00000174130), LRRC3B (ENSG00000179796), TSKU (ENSG00000182704), TLR5 (ENSG00000187554), TLR7 (ENSG00000196664), LRRC3C (ENSG00000204913)

Protein

Protein identifiers

Leucine-rich repeat, immunoglobulin-like domain and transmembrane domain-containing protein 2 — A6NDA9 (reviewed: A6NDA9)

Alternative names: Leucine-rich repeat-containing protein 22

All UniProt accessions (1): A6NDA9

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with LRIT1; may form a heterodimer with LRIT1.

Subcellular location. Membrane.

Isoforms (2)

UniProt ID	Names	Canonical?
A6NDA9-1	1	yes
A6NDA9-2	2

RefSeq proteins (2): NP_001017924, NP_001271152 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000483	Cys-rich_flank_reg_C	Domain
IPR001611	Leu-rich_rpt	Repeat
IPR003591	Leu-rich_rpt_typical-subtyp	Repeat
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR003961	FN3_dom	Domain
IPR007110	Ig-like_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR020901	Prtase_inh_Kunz-CS	Conserved_site
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050467	LRFN	Family

Pfam: PF00560, PF13855, PF13927

UniProt features (21 total): sequence variant 5, domain 4, repeat 4, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, glycosylation site 1, disulfide bond 1, splice variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NDA9-F1	77.76	0.44

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 274–327

Glycosylation sites (1): 52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 19 (showing top): chr10q23, MIR1277_5P, MIR570_3P, MIR4495, MIR876_5P, MIR3167, MIR8060, MIR365A_3P_MIR365B_3P, MIR4695_3P, MIR1287_5P, DESCARTES_MAIN_FETAL_PHOTORECEPTOR_CELLS, DESCARTES_FETAL_EYE_PHOTORECEPTOR_CELLS, WP_10Q22Q23_COPY_NUMBER_VARIATION, GSE2585_AIRE_KO_VS_WT_CD80_HIGH_MTEC_DN, GSE19888_ADENOSINE_A3R_INH_VS_TCELL_MEMBRANES_ACT_MAST_CELL_UP

GO Biological Process (0):

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

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

512 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRIT2	MANSC4	A6NHS7	671
LRIT2	CCDC126	Q96EE4	625
LRIT2	WDR17	Q8IZU2	575
LRIT2	FAM169A	Q9Y6X4	573
LRIT2	GPR15LG	Q6UWK7	571
LRIT2	PPEF2	O14830	570
LRIT2	TTC38	Q5R3I4	557
LRIT2	GRIFIN	A4D1Z8	556
LRIT2	DDX28	Q9NUL7	520
LRIT2	KCNJ14	Q9UNX9	518
LRIT2	CDHR1	Q96JP9	510
LRIT2	BMS1	Q14692	448
LRIT2	ARMC10	Q8N2F6	423
LRIT2	GHITM	Q9H3K2	417
LRIT2	DHX32	Q7L7V1	416

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LRIT2	SIGLEC10	psi-mi:“MI:0915”(physical association)	0.400

ESM2 similar proteins: A1A4H9, A2ARI4, A6NDA9, B0BLW3, B4F7C5, D3ZAL8, D3ZTV3, D4A6D8, D4A7P2, E7FE13, F1MT22, O14498, O43155, O43300, P0DM44, P83286, Q149C3, Q5NVQ6, Q5R6B1, Q5R7M3, Q5RAC4, Q6PFC5, Q6RKD8, Q80WD0, Q80XG9, Q80ZD7, Q80ZD8, Q80ZD9, Q810C0, Q810C1, Q86SJ2, Q86UE6, Q86UN2, Q86VH4, Q86VH5, Q86WK6, Q8BGA3, Q8BLU0, Q8BZ81, Q8C2S7

Diamond homologs: A0A087WV53, A1KZ92, A2AJ76, A4IFW2, A4IGL7, A6NDA9, B0BNK7, B0V2N1, D2HFT7, D3YXG0, D4A1J9, D4ABX8, F1NWE3, G5EG78, O15146, O73775, O75325, O94898, P07722, P15364, P20916, P20917, P23468, P43146, P48960, P53813, P70193, P70211, Q03142, Q08761, Q08879, Q13332, Q13449, Q1ENI8, Q1RMS4, Q1WIM1, Q21038, Q24372, Q26474, Q2Q421

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	100
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

409 predictions. Top by Δscore:

Variant	Effect	Δscore
10:84222679:CA:C	acceptor_gain	0.9900
10:84222681:C:CC	acceptor_gain	0.9900
10:84222685:G:GC	acceptor_gain	0.9800
10:84225423:T:A	donor_gain	0.9800
10:84222491:TCCGA:T	acceptor_gain	0.9700
10:84222492:C:G	acceptor_gain	0.9600
10:84222676:CAACA:C	acceptor_gain	0.9600
10:84222685:G:C	acceptor_gain	0.9600
10:84224642:C:CT	donor_gain	0.9500
10:84222677:AACA:A	acceptor_gain	0.9400
10:84225413:G:A	donor_gain	0.9300
10:84225405:GCGCA:G	donor_loss	0.9200
10:84225406:CGCA:C	donor_loss	0.9200
10:84225407:GCA:G	donor_loss	0.9200
10:84225408:CACC:C	donor_loss	0.9200
10:84225409:ACCT:A	donor_loss	0.9200
10:84222494:G:T	acceptor_gain	0.9100
10:84222678:ACA:A	acceptor_gain	0.9100
10:84222679:CAC:C	acceptor_gain	0.9100
10:84225440:T:TA	donor_gain	0.9100
10:84222677:AACAC:A	acceptor_loss	0.9000
10:84222678:ACAC:A	acceptor_loss	0.9000
10:84222679:CACTG:C	acceptor_loss	0.9000
10:84222680:ACT:A	acceptor_loss	0.9000
10:84222681:CT:C	acceptor_loss	0.9000
10:84222682:T:C	acceptor_loss	0.9000
10:84225115:C:CC	acceptor_gain	0.9000
10:84223231:T:C	acceptor_gain	0.8900
10:84224643:C:CT	donor_gain	0.8900
10:84225116:T:C	acceptor_loss	0.8800

AlphaMissense

3570 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:84224367:C:A	W286C	0.990
10:84224367:C:G	W286C	0.990
10:84224369:A:G	W286R	0.986
10:84224369:A:T	W286R	0.986
10:84222600:A:C	Y325D	0.984
10:84224619:C:A	W202C	0.983
10:84224619:C:G	W202C	0.983
10:84224404:C:G	C274S	0.977
10:84224405:A:T	C274S	0.977
10:84224621:A:G	W202R	0.977
10:84224621:A:T	W202R	0.977
10:84222429:A:G	W382R	0.975
10:84222429:A:T	W382R	0.975
10:84222632:A:G	I314T	0.975
10:84222593:C:G	C327S	0.974
10:84222594:A:T	C327S	0.974
10:84222580:G:C	N331K	0.973
10:84222580:G:T	N331K	0.973
10:84222229:A:C	F448L	0.971
10:84222229:A:T	F448L	0.971
10:84222231:A:G	F448L	0.971
10:84222230:A:C	F448C	0.970
10:84224405:A:G	C274R	0.970
10:84222599:T:G	Y325S	0.969
10:84222599:T:C	Y325C	0.968
10:84222592:G:C	C327W	0.961
10:84222600:A:T	Y325N	0.958
10:84222594:A:G	C327R	0.955
10:84224337:A:C	F296L	0.955
10:84224337:A:T	F296L	0.955

dbSNP variants (sampled 300 via entrez): RS1000886636 (10:84225193 C>G,T), RS1002289139 (10:84223780 T>C), RS1003074095 (10:84227448 G>T), RS1003365516 (10:84221811 A>G), RS1003613263 (10:84226826 AG>A,AGG), RS1003736529 (10:84223026 C>T), RS1004326190 (10:84227221 C>T), RS1004638084 (10:84222565 G>A,T), RS1004793530 (10:84222857 C>A,G), RS1005174230 (10:84222670 A>C,T), RS1005298519 (10:84225676 G>A), RS1005544121 (10:84227105 C>G,T), RS1005636622 (10:84221312 T>C), RS1005742701 (10:84226005 G>T), RS1005798812 (10:84220097 A>G,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

3 associations (top):

Study	Trait	p-value
GCST006291_113	Spherical equivalent or myopia (age of diagnosis)	9.000000e-17
GCST006976_130	Macular thickness	2.000000e-08
GCST010002_293	Refractive error	1.000000e-70

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004847	age at onset

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	decreases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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