CLEC20A

Summary

CLEC20A (C-type lectin domain containing 20A, HGNC:34521) is a protein-coding gene on chromosome 1q25.2, encoding Putative C-type lectin domain family 20 member A (Q6ZU45).

Predicted to enable carbohydrate binding activity.

Source: NCBI Gene 400797 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395331

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34521
Approved symbol	CLEC20A
Name	C-type lectin domain containing 20A
Location	1q25.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44005, RP4-593C16.2
Ensembl gene	ENSG00000188585
Ensembl biotype	protein_coding
Entrez	400797

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000445098, ENST00000623247, ENST00000641292, ENST00000646925

RefSeq mRNA: 1 — MANE Select: NM_001395331 NM_001395331

CCDS: CCDS91118

Canonical transcript exons

ENST00000623247 — 8 exons

Exon	Start	End
ENSE00003756418	178482312	178482397
ENSE00003791769	178490072	178490437
ENSE00003792490	178483175	178483282
ENSE00003794749	178488501	178488599
ENSE00003797537	178492501	178492566
ENSE00003800602	178494454	178494810
ENSE00003978281	178479240	178479615
ENSE00003978282	178496900	178496964

Expression profiles

Bgee: expression breadth broad, 45 present calls, max score 86.56.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.56	gold quality
left testis	UBERON:0004533	65.46	gold quality
testis	UBERON:0000473	65.11	gold quality
right testis	UBERON:0004534	64.79	gold quality
granulocyte	CL:0000094	57.72	gold quality
lymph node	UBERON:0000029	56.07	gold quality
bone marrow	UBERON:0002371	53.30	gold quality
tibial nerve	UBERON:0001323	52.79	gold quality
bone marrow cell	CL:0002092	49.18	gold quality
tonsil	UBERON:0002372	45.23	gold quality
sural nerve	UBERON:0015488	44.67	gold quality
gall bladder	UBERON:0002110	44.51	gold quality
stromal cell of endometrium	CL:0002255	44.06	gold quality
descending thoracic aorta	UBERON:0002345	43.80	silver quality
spleen	UBERON:0002106	43.58	gold quality
thoracic aorta	UBERON:0001515	42.61	gold quality
blood	UBERON:0000178	42.33	silver quality
ascending aorta	UBERON:0001496	42.24	gold quality
leukocyte	CL:0000738	41.60	silver quality
vermiform appendix	UBERON:0001154	41.21	gold quality
ventricular zone	UBERON:0003053	40.02	gold quality
monocyte	CL:0000576	39.54	gold quality
mucosa of stomach	UBERON:0001199	39.15	silver quality
urinary bladder	UBERON:0001255	38.05	gold quality
metanephros cortex	UBERON:0010533	37.83	gold quality
ganglionic eminence	UBERON:0004023	37.34	gold quality
small intestine Peyer’s patch	UBERON:0003454	37.22	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	36.97	silver quality
small intestine	UBERON:0002108	36.94	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.11

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Clec20a	ENSRNOG00000065155

Protein

Protein identifiers

Putative C-type lectin domain family 20 member A — Q6ZU45 (reviewed: Q6ZU45)

All UniProt accessions (2): A0A2R8Y4N8, Q6ZU45

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_001382260* (*=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

Pfam: PF00059

UniProt features (9 total): disulfide bond 4, domain 2, signal peptide 1, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZU45-F1	72.20	0.23

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 (4): 40–130, 105–122, 180–274, 248–266

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): chr1q25, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GOMF_CARBOHYDRATE_BINDING

GO Biological Process (0):

GO Molecular Function (1): carbohydrate binding (GO:0030246)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

88 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CLEC20A	NBDY	A0A0U1RRE5	447
CLEC20A	ATRN	O75882	311
CLEC20A	KRT9	P35527	305
CLEC20A	PSMA2	P25787	294
CLEC20A	PA2G4	Q9UQ80	280
CLEC20A	CLIP1	P30622	255
CLEC20A	PTGES3	Q15185	247
CLEC20A	KRT1	P04264	197
CLEC20A	CLSTN3	Q9BQT9	180
CLEC20A	WNT7A	O00755	179
CLEC20A	HSPA9	P30036	177
CLEC20A	COPS7A	Q9UBW8	174
CLEC20A	ANXA2	P07355	173
CLEC20A	AOAH	P28039	160
CLEC20A	ABCF1	Q8NE71	125

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6H6E2, A6QQC6, O43278, O55034, O88324, O89103, P02707, P06734, P0C6B7, P10716, P20693, P21757, P30203, P30204, P41274, P47970, P60883, P70194, P86176, Q01151, Q05585, Q5DID0, Q5DID3, Q5RFW0, Q61003, Q64335, Q6ZS10, Q6ZU45, Q86T13, Q8CFD9, Q8CJ91, Q8HY02, Q8HY04, Q8MIS5, Q8N1N0, Q8VCP9, Q91ZV2, Q91ZW7, Q91ZW8, Q91ZX1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2599 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:178490223:C:A	W226C	0.993
1:178490223:C:G	W226C	0.993
1:178494647:C:A	W68C	0.991
1:178494647:C:G	W68C	0.991
1:178494467:G:C	F128L	0.989
1:178494467:G:T	F128L	0.989
1:178494469:A:G	F128L	0.989
1:178494605:C:A	W82C	0.987
1:178494605:C:G	W82C	0.987
1:178494752:C:A	W33C	0.987
1:178494752:C:G	W33C	0.987
1:178494732:C:G	C40S	0.982
1:178494733:A:T	C40S	0.982
1:178490362:C:G	C180S	0.981
1:178490363:A:T	C180S	0.981
1:178490382:C:A	W173C	0.981
1:178490382:C:G	W173C	0.981
1:178490190:C:A	W237C	0.979
1:178490190:C:G	W237C	0.979
1:178490265:C:A	W212C	0.979
1:178490265:C:G	W212C	0.979
1:178494745:C:G	A36P	0.979
1:178490085:G:C	F272L	0.977
1:178490085:G:T	F272L	0.977
1:178490087:A:G	F272L	0.977
1:178490225:A:G	W226R	0.977
1:178490225:A:T	W226R	0.977
1:178494607:A:G	W82R	0.977
1:178494607:A:T	W82R	0.977
1:178494649:A:G	W68R	0.977

dbSNP variants (sampled 300 via entrez): RS1000028675 (1:178497647 A>G), RS1000055816 (1:178486789 AG>A), RS1000059997 (1:178497880 G>A), RS1000268262 (1:178483416 G>A), RS1000284725 (1:178480693 C>T), RS1000303604 (1:178483742 A>C,G,T), RS1000529901 (1:178486518 T>C,G), RS1000561446 (1:178494092 G>A,C), RS1000569985 (1:178482272 A>G), RS1000740211 (1:178489054 G>A), RS1001020593 (1:178497155 T>A,C), RS1001022415 (1:178499177 G>A), RS1001280122 (1:178485749 A>G), RS1001302169 (1:178479279 A>G), RS1001441823 (1:178496991 A>C)

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

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Permethrin	decreases expression	1

Clinical trials (associated diseases)

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