LANCL3

Summary

LANCL3 (LanC like family member 3, HGNC:24767) is a protein-coding gene on chromosome Xp21.1, encoding LanC-like protein 3 (Q6ZV70).

Predicted to be involved in carbohydrate metabolic process and peptide modification. Predicted to be active in plasma membrane.

Source: NCBI Gene 347404 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 79 total
• MANE Select transcript: NM_001170331

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24767
Approved symbol	LANCL3
Name	LanC like family member 3
Location	Xp21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ42925
Ensembl gene	ENSG00000147036
Ensembl biotype	protein_coding
Entrez	347404

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000378619, ENST00000378621, ENST00000614025

RefSeq mRNA: 2 — MANE Select: NM_001170331 NM_001170331, NM_198511

CCDS: CCDS14240, CCDS55398

Canonical transcript exons

ENST00000378619 — 5 exons

Exon	Start	End
ENSE00000978438	37655688	37655811
ENSE00000978439	37659462	37659659
ENSE00000978440	37667282	37667489
ENSE00001862882	37571661	37572443
ENSE00001957816	37675654	37684463

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 82.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1327 / max 20.8486, expressed in 56 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195892	0.1327	56

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
dorsal root ganglion	UBERON:0000044	82.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.46	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.32	gold quality
trigeminal ganglion	UBERON:0001675	73.12	gold quality
endothelial cell	CL:0000115	72.00	silver quality
middle temporal gyrus	UBERON:0002771	68.72	gold quality
Brodmann (1909) area 23	UBERON:0013554	66.27	gold quality
monocyte	CL:0000576	64.50	gold quality
leukocyte	CL:0000738	63.94	gold quality
esophagus squamous epithelium	UBERON:0006920	63.72	silver quality
primary visual cortex	UBERON:0002436	63.35	gold quality
palpebral conjunctiva	UBERON:0001812	63.20	silver quality
mucosa of transverse colon	UBERON:0004991	62.65	gold quality
gingival epithelium	UBERON:0001949	62.62	silver quality
cerebellar vermis	UBERON:0004720	60.73	gold quality
esophagus mucosa	UBERON:0002469	59.24	gold quality
lower esophagus mucosa	UBERON:0035834	59.10	gold quality
occipital lobe	UBERON:0002021	58.90	gold quality
transverse colon	UBERON:0001157	58.39	gold quality
muscle layer of sigmoid colon	UBERON:0035805	58.17	gold quality
prefrontal cortex	UBERON:0000451	58.03	gold quality
colonic epithelium	UBERON:0000397	57.01	silver quality
gingiva	UBERON:0001828	56.43	silver quality
colon	UBERON:0001155	56.13	gold quality
amniotic fluid	UBERON:0000173	55.90	silver quality
ileal mucosa	UBERON:0000331	55.82	silver quality
Brodmann (1909) area 9	UBERON:0013540	55.75	gold quality
large intestine	UBERON:0000059	55.65	gold quality
rectum	UBERON:0001052	55.42	gold quality
bone marrow cell	CL:0002092	55.41	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	44.53
E-ANND-3	no	5.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting LANCL3, 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-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-3941	99.86	70.54	2735
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-6079	99.84	68.54	1170
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-202-5P	99.78	67.65	991

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lancl3	ENSMUSG00000047344
rattus_norvegicus	Lancl3	ENSRNOG00000003756
drosophila_melanogaster	CG2061	FBGN0027498

Paralogs (2): LANCL1 (ENSG00000115365), LANCL2 (ENSG00000132434)

Protein

Protein identifiers

LanC-like protein 3 — Q6ZV70 (reviewed: Q6ZV70)

All UniProt accessions (1): Q6ZV70

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the LanC-like protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZV70-1	1	yes
Q6ZV70-2	2

RefSeq proteins (2): NP_001163802, NP_940913 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007822	LANC-like	Family
IPR012341	6hp_glycosidase-like_sf	Homologous_superfamily
IPR020464	LanC-like_prot_euk	Family

Pfam: PF05147

UniProt features (2 total): chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZV70-F1	93.66	0.88

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): GOBP_PEPTIDE_METABOLIC_PROCESS, KOYAMA_SEMA3B_TARGETS_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, ELK1_01, RGAGGAARY_PU1_Q6, YYCATTCAWW_UNKNOWN, RIGGI_EWING_SARCOMA_PROGENITOR_UP, MGGAAGTG_GABP_B, ETS_Q4, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, MEISSNER_BRAIN_HCP_WITH_H3K4ME2, chrXp21, GOBP_PEPTIDE_MODIFICATION, NFE2L2.V2

GO Biological Process (2): carbohydrate metabolic process (GO:0005975), peptide modification (GO:0031179)

GO Molecular Function (0):

GO Cellular Component (1): plasma membrane (GO:0005886)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
peptide metabolic process	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LANCL3	PRRG1	O14668	539
LANCL3	MAGEB16	A2A368	538
LANCL3	OR10H4	Q8NGA5	477
LANCL3	DYNLT3	P51808	475
LANCL3	FAM47B	Q8NA70	437
LANCL3	ECD	O95905	419
LANCL3	C12orf43	Q96C57	415
LANCL3	PMFBP1	Q8TBY8	373
LANCL3	TVP23A	A6NH52	371
LANCL3	CFAP47	Q6ZTR5	370
LANCL3	CPA6	Q8N4T0	348
LANCL3	TMEM47	Q9BQJ4	341
LANCL3	SYTL5	Q8TDW5	334
LANCL3	PLCXD1	Q9NUJ7	326
LANCL3	UBE2QL1	A1L167	317

IntAct

2 interactions, top by confidence:

A	B	Type	Score
LANCL3	RNF187	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): RNF187 (Affinity Capture-MS), LANCL3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A3KG59, A4IFH5, B9N1F9, D3ZVR9, O04059, O35331, O35621, O46560, P11172, P24298, P37111, Q03154, Q04609, Q15124, Q17QK3, Q2R483, Q501L1, Q5E9T8, Q5I0K3, Q5NAY4, Q5R514, Q5R5C9, Q5RDE7, Q5RDN7, Q5RFB0, Q5RFI8, Q6AY30, Q6AYS7, Q6K2E8, Q6PTT0, Q6Q0N1, Q6ZV70, Q7TSV4, Q7X7L3, Q8BZF8, Q8CG45, Q8CG76, Q8IYS1, Q8K183, Q8N0X4

Diamond homologs: F1MVX2, F4IEM5, O43813, O89112, Q29HZ1, Q6ZV70, Q8CD19, Q8VZQ6, Q90ZL2, Q9JJK2, Q9NS86, Q9QX69, Q9Y0Y7, Q9FJN7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	10
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1659 predictions. Top by Δscore:

Variant	Effect	Δscore
X:37572440:GGAG:G	donor_gain	1.0000
X:37572441:GAGG:G	donor_gain	1.0000
X:37572442:AGGT:A	donor_loss	1.0000
X:37572443:GGTAA:G	donor_loss	1.0000
X:37572445:T:G	donor_loss	1.0000
X:37655808:TTGGG:T	donor_loss	1.0000
X:37655809:TGGG:T	donor_loss	1.0000
X:37655810:GG:G	donor_gain	1.0000
X:37655811:GG:G	donor_gain	1.0000
X:37655811:GGT:G	donor_loss	1.0000
X:37655812:G:A	donor_loss	1.0000
X:37655812:G:GG	donor_gain	1.0000
X:37655813:T:TC	donor_loss	1.0000
X:37572441:GAG:G	donor_gain	0.9900
X:37572444:G:GG	donor_gain	0.9900
X:37601760:A:G	donor_gain	0.9900
X:37655683:TTCA:T	acceptor_loss	0.9900
X:37655684:TCA:T	acceptor_loss	0.9900
X:37655684:TCAG:T	acceptor_loss	0.9900
X:37655685:CA:C	acceptor_loss	0.9900
X:37655686:A:T	acceptor_loss	0.9900
X:37655687:G:GC	acceptor_loss	0.9900
X:37655807:CTTGG:C	donor_gain	0.9900
X:37655814:AAGT:A	donor_loss	0.9900
X:37656148:G:GT	donor_gain	0.9900
X:37656148:G:T	donor_gain	0.9900
X:37667277:CACA:C	acceptor_loss	0.9900
X:37667279:CA:C	acceptor_loss	0.9900
X:37667280:A:AC	acceptor_loss	0.9900
X:37667280:A:AG	acceptor_gain	0.9900

AlphaMissense

2691 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:37655739:G:T	G209W	1.000
X:37659641:T:A	W293R	1.000
X:37659641:T:C	W293R	1.000
X:37572376:A:T	E169V	0.999
X:37572387:G:C	G173R	0.999
X:37572388:G:A	G173D	0.999
X:37572388:G:T	G173V	0.999
X:37572390:C:A	R174S	0.999
X:37572391:G:C	R174P	0.999
X:37572396:G:C	G176R	0.999
X:37572397:G:A	G176D	0.999
X:37572397:G:T	G176V	0.999
X:37655740:G:A	G209E	0.999
X:37655805:T:C	Y231H	0.999
X:37655811:G:A	G233R	0.999
X:37655811:G:C	G233R	0.999
X:37655811:G:T	G233W	0.999
X:37659462:G:A	G233E	0.999
X:37659468:C:A	A235D	0.999
X:37659470:C:G	H236D	0.999
X:37659472:C:A	H236Q	0.999
X:37659472:C:G	H236Q	0.999
X:37659473:G:C	G237R	0.999
X:37659474:G:A	G237D	0.999
X:37659474:G:T	G237V	0.999
X:37659590:T:A	W276R	0.999
X:37659590:T:C	W276R	0.999
X:37659644:T:C	C294R	0.999
X:37659647:C:G	H295D	0.999
X:37659651:G:A	G296D	0.999

dbSNP variants (sampled 300 via entrez): RS1000097039 (X:37635445 A>G,T), RS1000149434 (X:37636137 A>G), RS1000291601 (X:37654681 A>C), RS1000412453 (X:37654417 G>C,T), RS1000497861 (X:37598899 T>C), RS1000525344 (X:37664624 G>A,C), RS1000633866 (X:37598512 T>C), RS1000691042 (X:37675174 A>C,G), RS1000714004 (X:37616982 A>G), RS1000810733 (X:37616447 C>G), RS1000923977 (X:37626266 A>G), RS1001099060 (X:37637964 C>G), RS1001135463 (X:37607883 G>T), RS1001150028 (X:37638291 A>G), RS1001249445 (X:37670399 A>G)

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

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, affects methylation	2
triphenyl phosphate	affects expression	1
sulforaphane	increases expression	1
ferrous chloride	increases expression	1
di-n-butylphosphoric acid	affects expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Catechin	increases expression, affects cotreatment	1
Diazinon	decreases methylation	1
Gallic Acid	decreases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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