LRRN4CL

Summary

LRRN4CL (LRRN4 C-terminal like, HGNC:33724) is a protein-coding gene on chromosome 11q12.3, encoding LRRN4 C-terminal-like protein (Q8ND94).

Predicted to be located in membrane.

Source: NCBI Gene 221091 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 44 total
• MANE Select transcript: NM_203422

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33724
Approved symbol	LRRN4CL
Name	LRRN4 C-terminal like
Location	11q12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000177363
Ensembl biotype	protein_coding
Entrez	221091

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000317449, ENST00000961805

RefSeq mRNA: 1 — MANE Select: NM_203422 NM_203422

CCDS: CCDS8030

Canonical transcript exons

ENST00000317449 — 2 exons

Exon	Start	End
ENSE00001412494	62689427	62689530
ENSE00001413046	62686406	62688513

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 93.62.

FANTOM5 (CAGE): breadth broad, TPM avg 8.5820 / max 311.8240, expressed in 696 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120199	8.5820	696

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	93.62	gold quality
skin of hip	UBERON:0001554	92.90	gold quality
mucosa of stomach	UBERON:0001199	89.20	gold quality
tendon of biceps brachii	UBERON:0008188	88.78	gold quality
cauda epididymis	UBERON:0004360	88.03	gold quality
body of uterus	UBERON:0009853	87.74	gold quality
adipose tissue	UBERON:0001013	86.82	gold quality
parietal pleura	UBERON:0002400	86.81	gold quality
endocervix	UBERON:0000458	86.74	gold quality
stromal cell of endometrium	CL:0002255	86.68	gold quality
tendon	UBERON:0000043	86.19	gold quality
left uterine tube	UBERON:0001303	86.03	gold quality
subcutaneous adipose tissue	UBERON:0002190	85.91	gold quality
adipose tissue of abdominal region	UBERON:0007808	85.76	gold quality
right ovary	UBERON:0002118	85.68	gold quality
omental fat pad	UBERON:0010414	85.58	gold quality
left ovary	UBERON:0002119	85.53	gold quality
peritoneum	UBERON:0002358	85.51	gold quality
calcaneal tendon	UBERON:0003701	85.36	gold quality
ectocervix	UBERON:0012249	84.89	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.30	gold quality
upper leg skin	UBERON:0004262	84.24	gold quality
mammalian vulva	UBERON:0000997	84.07	gold quality
lower esophagus muscularis layer	UBERON:0035833	83.80	gold quality
lower esophagus	UBERON:0013473	83.69	gold quality
synovial joint	UBERON:0002217	83.49	gold quality
myometrium	UBERON:0001296	83.41	gold quality
vena cava	UBERON:0004087	83.21	gold quality
uterine cervix	UBERON:0000002	82.74	gold quality
layer of synovial tissue	UBERON:0007616	82.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	15.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

41 targeting LRRN4CL, 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-4283	100.00	66.42	2097
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-6849-5P	99.64	66.00	352
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-6797-3P	99.17	66.94	668
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6889-3P	98.84	67.35	1198

Literature-anchored findings (GeneRIF, showing 1)

• CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation. (PMID:33758365)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch1073-303k11.2	ENSDARG00000088247
danio_rerio		ENSDARG00000116863
mus_musculus	Lrrn4cl	ENSMUSG00000071656

Paralogs (3): LRRN4 (ENSG00000125872), ISLR (ENSG00000129009), ISLR2 (ENSG00000167178)

Protein

Protein identifiers

LRRN4 C-terminal-like protein — Q8ND94 (reviewed: Q8ND94)

All UniProt accessions (1): Q8ND94

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_981967* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003961	FN3_dom	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036116	FN3_sf	Homologous_superfamily

Pfam: PF00041

UniProt features (8 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, glycosylation site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8ND94-F1	81.60	0.61

Functional residue map

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

Glycosylation sites (1): 132

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, ROZANOV_MMP14_TARGETS_UP, TGANTCA_AP1_C, TGACATY_UNKNOWN, ATF4_Q2, TGGNNNNNNKCCAR_UNKNOWN, TTCNRGNNNNTTC_HSF_Q6, TGGAAA_NFAT_Q4_01, WGGAATGY_TEF1_Q6, MIKKELSEN_ES_ICP_WITH_H3K4ME3, AP1_Q6_01, ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR, GSE10094_LCMV_VS_LISTERIA_IND_EFF_CD4_TCELL_DN

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

524 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRN4CL	TM4SF19	Q96DZ7	472
LRRN4CL	PDCL2	Q8N4E4	453
LRRN4CL	SAPCD2	Q86UD0	396
LRRN4CL	SLC4A3	P48751	393
LRRN4CL	SLC25A47	Q6Q0C1	393
LRRN4CL	IGSF9B	Q9UPX0	393
LRRN4CL	TMEM45B	Q96B21	385
LRRN4CL	TLCD4	Q96MV1	382
LRRN4CL	DGLUCY	Q7Z3D6	379
LRRN4CL	EML3	Q32P44	377
LRRN4CL	FABP12	A6NFH5	367
LRRN4CL	SERPINB11	Q96P15	363
LRRN4CL	TMEM116	Q8NCL8	351
LRRN4CL	SPART	Q8N0X7	348
LRRN4CL	PCBD2	Q9H0N5	347

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SRPK2	LRRN4CL	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
LRRN4CL	TCAF2	psi-mi:“MI:0914”(association)	0.350
LRRN4CL	BTAF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (62): PODXL2 (Affinity Capture-MS), GHITM (Affinity Capture-MS), FAM115C (Affinity Capture-MS), TM9SF3 (Affinity Capture-MS), OCLN (Affinity Capture-MS), SEMA4C (Affinity Capture-MS), IMMT (Affinity Capture-MS), EPHA1 (Affinity Capture-MS), MAP2K2 (Affinity Capture-MS), SRPR (Affinity Capture-MS), WDR11 (Affinity Capture-MS), SOAT1 (Affinity Capture-MS), CDS2 (Affinity Capture-MS), ERGIC1 (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS)

ESM2 similar proteins: A4FV93, A5A8Y8, B2LW77, D3ZUK3, O00468, O70534, O75074, O88204, O88839, O95407, P06579, P07204, P15306, P60882, P80370, Q09163, Q13444, Q14162, Q3SWY4, Q501P1, Q53RD9, Q5ND28, Q5VY43, Q5W7P8, Q61810, Q6AZ60, Q6GUQ1, Q6MG84, Q6UY11, Q71U07, Q75N90, Q7Z7M0, Q8K1E3, Q8K1S7, Q8K4G1, Q8NCW0, Q8ND94, Q8VIK5, Q8WUT4, Q93038

Diamond homologs: B1H234, D4ABX8, D4AC13, O46378, P02751, P12024, P59383, Q28256, Q3SWY4, Q3TYX2, Q4R8Y9, Q5S006, Q63912, Q6PEZ8, Q6PJG9, Q6QMY6, Q7TQ62, Q7Z5L7, Q8BGT1, Q8CBR6, Q8ND94, Q8WUT4, Q9NR97, Q9TTB4, P50608, P50609, P51890, Q06828, Q6P3Y9, Q80XU8, Q86SJ2, Q9CRC8, Q9DE67

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

305 predictions. Top by Δscore:

Variant	Effect	Δscore
11:62688514:C:CC	acceptor_gain	0.9900
11:62688453:C:G	acceptor_gain	0.9500
11:62688512:GA:G	acceptor_gain	0.9500
11:62688509:GGAGA:G	acceptor_gain	0.9200
11:62688510:GAGA:G	acceptor_gain	0.9200
11:62688512:GACTG:G	acceptor_loss	0.9200
11:62688513:ACTG:A	acceptor_loss	0.9200
11:62688514:C:T	acceptor_loss	0.9200
11:62688515:T:A	acceptor_loss	0.9200
11:62689419:CTCCT:C	donor_loss	0.9000
11:62689421:CCT:C	donor_loss	0.9000
11:62689422:CTCA:C	donor_loss	0.9000
11:62689423:TCACC:T	donor_loss	0.9000
11:62689424:C:CC	donor_loss	0.9000
11:62689425:A:AA	donor_loss	0.9000
11:62689426:C:A	donor_loss	0.9000
11:62689425:A:AC	donor_gain	0.8800
11:62689426:C:CC	donor_gain	0.8800
11:62688516:G:C	acceptor_loss	0.8500
11:62688483:C:CT	acceptor_gain	0.8300
11:62688609:C:CC	acceptor_gain	0.8300
11:62689069:TG:T	donor_gain	0.8300
11:62689393:C:A	donor_gain	0.8000
11:62689360:T:TA	donor_gain	0.7900
11:62688452:T:TG	acceptor_gain	0.7800
11:62688450:GCTCT:G	acceptor_gain	0.7700
11:62689076:G:A	donor_gain	0.7700
11:62689435:AGG:A	donor_gain	0.7600
11:62688511:AGA:A	acceptor_gain	0.7500
11:62688453:C:CC	acceptor_gain	0.7300

AlphaMissense

1501 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:62688197:C:A	W104C	0.998
11:62688197:C:G	W104C	0.998
11:62688103:G:T	R136S	0.991
11:62688199:A:G	W104R	0.991
11:62688199:A:T	W104R	0.991
11:62688195:C:G	C105S	0.987
11:62688196:A:T	C105S	0.987
11:62688261:G:T	P83H	0.987
11:62688039:T:A	N157I	0.985
11:62688045:G:T	A155D	0.984
11:62688054:C:T	C152Y	0.984
11:62688189:G:T	P107H	0.984
11:62687879:G:C	S210R	0.983
11:62687879:G:T	S210R	0.983
11:62687881:T:G	S210R	0.983
11:62688252:G:T	P86Q	0.983
11:62688330:C:G	C60S	0.982
11:62688331:A:T	C60S	0.982
11:62688054:C:G	C152S	0.981
11:62688055:A:T	C152S	0.981
11:62688204:A:T	V102D	0.981
11:62688291:C:G	C73S	0.981
11:62688292:A:T	C73S	0.981
11:62688351:C:G	C53S	0.981
11:62688352:A:T	C53S	0.981
11:62688023:G:C	S162R	0.980
11:62688023:G:T	S162R	0.980
11:62688025:T:G	S162R	0.980
11:62688168:T:C	Y114C	0.980
11:62688366:C:G	C48S	0.979

dbSNP variants (sampled 300 via entrez): RS1000210611 (11:62687734 G>A,C), RS1000536287 (11:62690867 C>G,T), RS1001122280 (11:62689390 C>T), RS1001791392 (11:62689984 G>A,C), RS1003247907 (11:62687730 C>G,T), RS1004340837 (11:62688734 G>A), RS1004545791 (11:62690470 G>A,C), RS1005091205 (11:62688392 C>A,T), RS1005576882 (11:62688594 G>A,T), RS1005734433 (11:62690169 G>A), RS1005960254 (11:62688993 CAG>C), RS1007078676 (11:62690836 T>C), RS1007680336 (11:62685977 T>G), RS1008041487 (11:62686235 C>T), RS1008431126 (11:62686968 C>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

4 associations (top):

Study	Trait	p-value
GCST005956_12	Waist-to-hip ratio adjusted for BMI	2.000000e-06
GCST005956_2	Waist-to-hip ratio adjusted for BMI	1.000000e-08
GCST005962_37	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	5.000000e-07
GCST005962_51	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-07

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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
methylmercuric chloride	increases expression	1
bisphenol A	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Dexamethasone	increases expression	1
Formaldehyde	increases expression	1
Latex	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
1-Methyl-4-phenylpyridinium	decreases expression	1
Aflatoxin B1	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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