CLEC19A

Summary

CLEC19A (C-type lectin domain containing 19A, HGNC:34522) is a protein-coding gene on chromosome 16p12.3, encoding C-type lectin domain family 19 member A (Q6UXS0).

Predicted to enable carbohydrate binding activity. Predicted to be located in extracellular region.

Source: NCBI Gene 728276 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 7 total
• MANE Select transcript: NM_001256720

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34522
Approved symbol	CLEC19A
Name	C-type lectin domain containing 19A
Location	16p12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000261210
Ensembl biotype	protein_coding
Entrez	728276

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000465414, ENST00000468219, ENST00000476906, ENST00000493231, ENST00000636231

RefSeq mRNA: 1 — MANE Select: NM_001256720 NM_001256720

CCDS: CCDS81953

Canonical transcript exons

ENST00000636231 — 5 exons

Exon	Start	End
ENSE00001817404	19298673	19298838
ENSE00003751781	19304062	19304155
ENSE00003753980	19285731	19285939
ENSE00003797847	19309004	19310947
ENSE00003798195	19307545	19307677

Expression profiles

Bgee: expression breadth broad, 63 present calls, max score 66.12.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3416 / max 32.4845, expressed in 108 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152999	0.1818	76
152998	0.1598	75

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	66.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.04	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	57.61	gold quality
mucosa of transverse colon	UBERON:0004991	56.11	gold quality
substantia nigra	UBERON:0002038	50.41	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	47.02	gold quality
hypothalamus	UBERON:0001898	46.91	gold quality
rectum	UBERON:0001052	46.20	gold quality
colonic epithelium	UBERON:0000397	46.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	45.87	gold quality
endometrium	UBERON:0001295	45.14	silver quality
prefrontal cortex	UBERON:0000451	44.66	gold quality
ganglionic eminence	UBERON:0004023	44.62	silver quality
skeletal muscle tissue	UBERON:0001134	44.50	gold quality
temporal lobe	UBERON:0001871	43.93	gold quality
Ammon’s horn	UBERON:0001954	43.71	gold quality
amygdala	UBERON:0001876	43.65	gold quality
lung	UBERON:0002048	43.22	gold quality
transverse colon	UBERON:0001157	42.91	gold quality
upper lobe of left lung	UBERON:0008952	42.61	gold quality
muscle of leg	UBERON:0001383	42.50	gold quality
muscle tissue	UBERON:0002385	42.32	gold quality
prostate gland	UBERON:0002367	42.12	gold quality
anterior cingulate cortex	UBERON:0009835	41.92	gold quality
minor salivary gland	UBERON:0001830	41.66	gold quality
stomach	UBERON:0000945	41.41	gold quality
gastrocnemius	UBERON:0001388	41.38	silver quality
ventricular zone	UBERON:0003053	41.36	gold quality
frontal cortex	UBERON:0001870	41.27	gold quality
gall bladder	UBERON:0002110	41.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting CLEC19A, 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-3613-3P	100.00	76.36	7965
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-153-5P	99.89	73.86	6317
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-567	99.63	68.57	1219
HSA-MIR-6757-3P	99.63	66.88	1089
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-6828-5P	99.31	69.21	1433
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-5690	99.25	67.58	1012
HSA-MIR-5693	99.24	66.67	1106
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-452-3P	99.01	66.25	1241

Literature-anchored findings (GeneRIF, showing 1)

• CLEC19A overexpression inhibits tumor cell proliferation/migration and promotes apoptosis concomitant suppression of PI3K/AKT/NF-kappaB signaling pathway in glioblastoma multiforme. (PMID:38167030)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	clec19a	ENSDARG00000115545
caenorhabditis_elegans		WBGENE00019914

Paralogs (5): REG1A (ENSG00000115386), REG4 (ENSG00000134193), REG3G (ENSG00000143954), REG3A (ENSG00000172016), REG1B (ENSG00000172023)

Protein

Protein identifiers

C-type lectin domain family 19 member A — Q6UXS0 (reviewed: Q6UXS0)

All UniProt accessions (3): Q6UXS0, H3BQW0, H3BQX8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UXS0-1	1	yes
Q6UXS0-2	2

RefSeq proteins (1): NP_001243649* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001304	C-type_lectin-like	Domain
IPR016186	C-type_lectin-like/link_sf	Homologous_superfamily
IPR016187	CTDL_fold	Homologous_superfamily
IPR018378	C-type_lectin_CS	Conserved_site
IPR033988	CEL1-like_CTLD	Domain
IPR050111	C-type_lectin/snaclec_domain	Family

Pfam: PF00059

UniProt features (9 total): disulfide bond 2, splice variant 2, signal peptide 1, chain 1, domain 1, glycosylation site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXS0-F1	85.51	0.67

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 (2): 68–178, 151–170

Glycosylation sites (1): 58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): chr16p12, ZNF92_TARGET_GENES, MIR153_5P, MIR4307, MIR4666A_5P, MIR4782_5P, MIR5706, MIR4437, GAO_LARGE_INTESTINE_ADULT_CE_OLFM4HIGH_STEM_CELL, DESCARTES_MAIN_FETAL_MICROGLIA, DESCARTES_FETAL_CEREBELLUM_MICROGLIA, DESCARTES_FETAL_CEREBRUM_MICROGLIA, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, NABA_ECM_AFFILIATED, NABA_MATRISOME_ASSOCIATED

GO Biological Process (0):

GO Molecular Function (2): carbohydrate binding (GO:0030246), protein binding (GO:0005515)

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cellular anatomical structure	1

Protein interactions and networks

STRING

242 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC19A	TM9SF2	Q99805	624
CLEC19A	FNDC7	Q5VTL7	589
CLEC19A	ABHD12B	Q7Z5M8	578
CLEC19A	ZC3H10	Q96K80	559
CLEC19A	CBLN3	Q6UW01	555
CLEC19A	TMEM69	Q5SWH9	549
CLEC19A	RBMS3	Q6XE24	545
CLEC19A	C1QTNF7	Q9BXJ2	543
CLEC19A	CCDC137	Q6PK04	532
CLEC19A	PECR	Q9BY49	502
CLEC19A	SLC15A4	Q8N697	468
CLEC19A	GOLGA8K	D6RF30	447
CLEC19A	ZPLD1	Q8TCW7	431
CLEC19A	LAMB4	A4D0S4	428
CLEC19A	GOLGA6L10	A6NI86	420

IntAct

4 interactions, top by confidence:

A	B	Type	Score
UBXN7	CLEC19A	psi-mi:“MI:0915”(physical association)	0.560
UBXN7	CLEC19A	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A0A1D5PUP4, O60242, O75882, O95970, P05452, P07306, P09858, P0C7M9, P15209, P21214, P24786, P25291, P27090, P37173, P43025, P51641, P61811, P61812, P78539, Q0ZCA7, Q1EGL2, Q2KIS7, Q2LK94, Q38L25, Q3SXB8, Q4TU93, Q5R7T2, Q5R945, Q5RBQ8, Q5RKH0, Q5VV63, Q62312, Q63604, Q63769, Q64449, Q6A051, Q6UXF7, Q6UXS0, Q80ZF8, Q8N475

Diamond homologs: A1XXJ9, A3FM55, A7X3W1, A7X3W6, A7X3X0, A7X3X3, A7X3X8, A7X3Y2, A7X3Y6, A7X3Z0, A7X3Z4, A7X3Z7, A7X401, A7X406, A7X409, A7X413, B0VXV0, B0VXV1, B5U6Y6, C6JUN9, D1MGU0, D2YVH7, D2YVI2, D2YVJ6, D2YVJ8, D2YVK1, D2YVK5, D2YW40, D8VNS6, I7ICN3, J3S3U6, J3SBP0, O93427, P05451, P07439, P0DL30, P0DM36, P0DM38, P0DM39, P0DM53

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

393 predictions. Top by Δscore:

Variant	Effect	Δscore
16:19285936:CCAGG:C	donor_loss	0.9900
16:19285938:AGGT:A	donor_loss	0.9900
16:19285940:GTAA:G	donor_loss	0.9900
16:19285941:T:A	donor_loss	0.9900
16:19298671:A:AG	acceptor_gain	0.9900
16:19298672:G:GG	acceptor_gain	0.9900
16:19285940:G:GG	donor_gain	0.9800
16:19295978:GGACC:G	donor_gain	0.9800
16:19298836:CAGG:C	donor_loss	0.9700
16:19298837:AGG:A	donor_loss	0.9700
16:19298838:GGTA:G	donor_loss	0.9700
16:19298839:GT:G	donor_loss	0.9700
16:19298840:T:A	donor_loss	0.9700
16:19295979:GACC:G	donor_gain	0.9600
16:19298672:GCCCT:G	acceptor_gain	0.9600
16:19285935:TCCAG:T	donor_gain	0.9400
16:19287311:G:GG	donor_gain	0.9400
16:19298760:A:G	acceptor_gain	0.9400
16:19285938:AG:A	donor_gain	0.9300
16:19285939:GG:G	donor_gain	0.9300
16:19298672:GCC:G	acceptor_gain	0.9300
16:19295975:G:GT	donor_gain	0.9100
16:19298672:GCCC:G	acceptor_gain	0.9100
16:19287310:A:AG	donor_gain	0.9000
16:19298669:CCAG:C	acceptor_loss	0.8800
16:19298670:CA:C	acceptor_loss	0.8800
16:19298671:A:T	acceptor_loss	0.8800
16:19287309:GA:G	donor_gain	0.8700
16:19298672:GC:G	acceptor_gain	0.8700
16:19298756:A:AG	acceptor_gain	0.8700

AlphaMissense

1236 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:19298723:T:C	F47L	0.989
16:19298725:C:A	F47L	0.989
16:19298725:C:G	F47L	0.989
16:19298795:T:C	F71L	0.988
16:19298797:C:A	F71L	0.988
16:19298797:C:G	F71L	0.988
16:19298774:G:C	A64P	0.987
16:19298767:G:C	W61C	0.984
16:19298767:G:T	W61C	0.984
16:19304078:T:C	F91L	0.982
16:19304080:T:A	F91L	0.982
16:19304080:T:G	F91L	0.982
16:19298742:G:C	R53P	0.981
16:19304091:T:C	L95P	0.979
16:19298716:G:C	W44C	0.977
16:19298716:G:T	W44C	0.977
16:19298744:T:C	F54L	0.971
16:19298746:C:A	F54L	0.971
16:19298746:C:G	F54L	0.971
16:19298738:T:G	Y52D	0.968
16:19298747:T:C	F55L	0.964
16:19298749:C:A	F55L	0.964
16:19298749:C:G	F55L	0.964
16:19298788:T:G	C68W	0.964
16:19304079:T:G	F91C	0.959
16:19298735:T:A	C51S	0.958
16:19298736:G:C	C51S	0.958
16:19304131:G:C	W108C	0.955
16:19304131:G:T	W108C	0.955
16:19304129:T:A	W108R	0.954

dbSNP variants (sampled 300 via entrez): RS1000099485 (16:19293981 T>C), RS1000146555 (16:19284309 C>A,T), RS1000253642 (16:19290478 C>T), RS1000316230 (16:19311110 T>C), RS1000517488 (16:19289507 A>G), RS1000911988 (16:19293682 C>T), RS1000913959 (16:19300228 A>C), RS1000946863 (16:19307942 T>TG), RS1001130749 (16:19294957 G>A), RS1001182400 (16:19292100 C>A), RS1001219747 (16:19293598 G>T), RS1001230875 (16:19287763 A>C), RS1001251621 (16:19300045 G>A), RS1001454416 (16:19304501 G>A,C), RS1001523437 (16:19283772 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

4 associations (top):

Study	Trait	p-value
GCST003484_1	Periodontal disease-related phenotype (Socransky)	3.000000e-10
GCST003984_17	Parkinson’s disease	1.000000e-08
GCST004068_70	Venous thromboembolism adjusted for sickle cell variant rs77121243-T	7.000000e-06
GCST006300_3	Smoking behaviour (maximum cigarettes in a 24 hour period)	7.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007780	periodontal measurement
EFO:0009264	maximum cigarettes per day measurement

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
Benzo(a)pyrene	increases methylation, decreases expression	2
butyraldehyde	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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