CD164L2

Summary

CD164L2 (CD164 molecule like 2, HGNC:32043) is a protein-coding gene on chromosome 1p36.11, encoding CD164 sialomucin-like 2 protein (Q6UWJ8).

Predicted to be located in membrane. Predicted to be active in cytoplasmic vesicle.

Source: NCBI Gene 388611 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_001330448

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32043
Approved symbol	CD164L2
Name	CD164 molecule like 2
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000174950
Ensembl biotype	protein_coding
Entrez	388611

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000374025, ENST00000374027, ENST00000374030, ENST00000884190, ENST00000966173

RefSeq mRNA: 2 — MANE Select: NM_001330448 NM_001330448, NM_207397

CCDS: CCDS302, CCDS81287

Canonical transcript exons

ENST00000374030 — 6 exons

Exon	Start	End
ENSE00001206451	27382328	27382399
ENSE00001329364	27381780	27381824
ENSE00001462198	27379176	27379509
ENSE00001462199	27380051	27380195
ENSE00001462200	27383152	27383333
ENSE00003753256	27382500	27382667

Expression profiles

Bgee: expression breadth ubiquitous, 107 present calls, max score 97.05.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2374 / max 21.4889, expressed in 106 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11228	0.1543	72
11227	0.0831	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.05	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.68	gold quality
esophagus mucosa	UBERON:0002469	86.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.90	gold quality
lower esophagus mucosa	UBERON:0035834	83.67	gold quality
fallopian tube	UBERON:0003889	80.48	gold quality
skin of leg	UBERON:0001511	80.27	gold quality
zone of skin	UBERON:0000014	79.59	gold quality
skin of abdomen	UBERON:0001416	78.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.30	silver quality
saliva-secreting gland	UBERON:0001044	77.75	gold quality
minor salivary gland	UBERON:0001830	77.16	gold quality
right lung	UBERON:0002167	73.45	gold quality
vagina	UBERON:0000996	71.29	gold quality
tonsil	UBERON:0002372	69.82	gold quality
left uterine tube	UBERON:0001303	66.53	gold quality
pituitary gland	UBERON:0000007	66.33	gold quality
upper lobe of left lung	UBERON:0008952	65.05	gold quality
prostate gland	UBERON:0002367	64.75	gold quality
lung	UBERON:0002048	63.57	gold quality
adenohypophysis	UBERON:0002196	62.27	gold quality
esophagus	UBERON:0001043	60.20	gold quality
uterine cervix	UBERON:0000002	56.07	gold quality
ectocervix	UBERON:0012249	56.00	gold quality
body of pancreas	UBERON:0001150	55.74	gold quality
thoracic mammary gland	UBERON:0005200	53.98	gold quality
body of stomach	UBERON:0001161	51.87	gold quality
endocervix	UBERON:0000458	51.16	gold quality
pancreas	UBERON:0001264	50.88	gold quality
right lobe of thyroid gland	UBERON:0001119	49.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting CD164L2, 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-4534	99.99	66.58	1907
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4284	99.36	65.25	1293
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-4641	99.28	66.64	744
HSA-MIR-4721	99.26	66.05	818
HSA-MIR-4784	99.15	67.41	1733
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-3150B-3P	98.81	67.21	1728
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-6864-5P	98.38	66.59	1079
HSA-MIR-3179	98.22	65.90	1445
HSA-MIR-4436A	98.05	64.83	1140
HSA-MIR-6787-3P	97.75	66.17	1233
HSA-MIR-9851-5P	97.57	67.49	1067
HSA-MIR-505-5P	97.01	65.54	778
HSA-MIR-597-3P	96.46	68.03	1035
HSA-MIR-6834-5P	96.25	64.88	823
HSA-MIR-7108-3P	94.37	64.79	183

Literature-anchored findings (GeneRIF, showing 1)

• Found that a common variant of FCN3/CD164L2 is associated with hypertension in Chinese population. (PMID:22471352)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cd164l2	ENSDARG00000096327
mus_musculus	Cd164l2	ENSMUSG00000028865
rattus_norvegicus	Cd164l2	ENSRNOG00000009505
drosophila_melanogaster	vsg	FBGN0045823

Paralogs (2): CD164 (ENSG00000135535), TMEM123 (ENSG00000152558)

Protein

Protein identifiers

CD164 sialomucin-like 2 protein — Q6UWJ8 (reviewed: Q6UWJ8)

All UniProt accessions (1): Q6UWJ8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the CD164 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6UWJ8-1	1	yes
Q6UWJ8-2	2

RefSeq proteins (2): NP_001317377, NP_997280 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007947	CD164_MGC24	Family

Pfam: PF05283

UniProt features (10 total): topological domain 2, glycosylation site 2, signal peptide 1, chain 1, transmembrane region 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UWJ8-F1	65.70	0.03

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 (2): 71, 103

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): CAGCAGG_MIR370, CTGAGCC_MIR24, chr1p36, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3K4ME2, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, MARTENS_TRETINOIN_RESPONSE_UP, GSE14415_NATURAL_TREG_VS_FOXP3_KO_NATURAL_TREG_UP, MIR765, MIR7515, MIR6768_5P, MIR11181_3P, FAN_EMBRYONIC_CTX_BIG_GROUPS_CAJAL_RETZIUS, GAO_ESOPHAGUS_25W_C1_CILIATED_EPITHELIAL_CELLS, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS

GO Biological Process (0):

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

GO Cellular Component (2): membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

202 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CD164L2	TEKT3	Q9BXF9	647
CD164L2	CCER2	I3L3R5	543
CD164L2	DCTN5	Q9BTE1	507
CD164L2	ADGRF3	Q8IZF5	502
CD164L2	EMID1	Q96A84	447
CD164L2	RPRD2	Q5VT52	429
CD164L2	CLEC12B	Q2HXU8	427
CD164L2	ACBD7	Q8N6N7	425
CD164L2	ABHD12B	Q7Z5M8	401
CD164L2	OC90	Q02509	390
CD164L2	HPS3	Q969F9	369
CD164L2	GNG8	Q9UK08	357
CD164L2	MATN4	O95460	325
CD164L2	ME1	P48163	320
CD164L2	CCDC141	Q6ZP82	312

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CD164L2	SLC19A1	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): SLC19A1 (Affinity Capture-MS), ARL5B (Affinity Capture-MS), LETMD1 (Affinity Capture-MS), RRAGB (Affinity Capture-MS), EMC7 (Affinity Capture-MS), LETMD1 (Affinity Capture-MS), SLC19A1 (Affinity Capture-MS), RRAGB (Affinity Capture-MS), USP30 (Affinity Capture-MS), ARL5B (Affinity Capture-MS), CD164L2 (Two-hybrid), CD164L2 (Two-hybrid), CD164L2 (Affinity Capture-MS), SLC19A1 (Affinity Capture-MS), LETMD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GW64, A0A5F4BST2, A0PJX4, A8MVS5, A8MWV9, B0FP48, E5RIL1, E9PGG2, O14836, O60320, O95998, P09564, Q01113, Q01114, Q13477, Q2KI80, Q2T9R2, Q3TS39, Q3UPR0, Q3URD2, Q4V9L6, Q5FVJ4, Q5M869, Q6A044, Q6UWJ8, Q75VT8, Q864V4, Q8BRJ3, Q8BX43, Q8C503, Q8IVY1, Q8K5A9, Q8N112, Q8NC24, Q8NDY8, Q8QZT4, Q8R138, Q969Z4, Q9BUF7, Q9CQM1

Diamond homologs: Q04900, Q2YDH0, Q6UWJ8, Q9D6W7, Q9QX82, Q9R0L9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

917 predictions. Top by Δscore:

Variant	Effect	Δscore
1:27380194:CC:C	acceptor_gain	1.0000
1:27380195:CC:C	acceptor_gain	1.0000
1:27382678:G:T	acceptor_gain	1.0000
1:27379328:C:CT	acceptor_gain	0.9900
1:27379328:C:T	acceptor_gain	0.9900
1:27380049:A:AC	donor_gain	0.9900
1:27380050:C:CC	donor_gain	0.9900
1:27380050:CAG:C	donor_gain	0.9900
1:27380191:GCTCC:G	acceptor_gain	0.9900
1:27380192:CTCC:C	acceptor_gain	0.9900
1:27380192:CTCCC:C	acceptor_gain	0.9900
1:27380193:TCC:T	acceptor_gain	0.9900
1:27380193:TCCCT:T	acceptor_gain	0.9900
1:27380194:CCC:C	acceptor_gain	0.9900
1:27380196:C:CC	acceptor_gain	0.9900
1:27380197:T:C	acceptor_loss	0.9900
1:27382322:CCTTA:C	donor_loss	0.9900
1:27382323:CTTAC:C	donor_loss	0.9900
1:27382324:TTAC:T	donor_loss	0.9900
1:27382325:TACCT:T	donor_loss	0.9900
1:27382326:ACCT:A	donor_loss	0.9900
1:27382327:C:CG	donor_loss	0.9900
1:27382494:CCATA:C	donor_loss	0.9900
1:27382495:CATA:C	donor_loss	0.9900
1:27382496:ATACC:A	donor_loss	0.9900
1:27382497:TACC:T	donor_loss	0.9900
1:27382498:A:C	donor_loss	0.9900
1:27382499:CCTGG:C	donor_gain	0.9900
1:27382677:C:CT	acceptor_gain	0.9900
1:27382679:G:GC	acceptor_gain	0.9900

AlphaMissense

1111 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:27382525:C:A	W77C	0.989
1:27382525:C:G	W77C	0.989
1:27380116:G:C	S151R	0.974
1:27380116:G:T	S151R	0.974
1:27380118:T:G	S151R	0.974
1:27380158:A:C	F137L	0.935
1:27380158:A:T	F137L	0.935
1:27380160:A:G	F137L	0.935
1:27380146:G:C	S141R	0.930
1:27380146:G:T	S141R	0.930
1:27380148:T:G	S141R	0.930
1:27382527:A:G	W77R	0.917
1:27382527:A:T	W77R	0.917
1:27382393:C:G	C88S	0.913
1:27382394:A:T	C88S	0.913
1:27380143:A:C	F142L	0.889
1:27380143:A:T	F142L	0.889
1:27380145:A:G	F142L	0.889
1:27382393:C:T	C88Y	0.888
1:27382392:A:C	C88W	0.871
1:27382568:C:T	C63Y	0.869
1:27382568:C:G	C63S	0.867
1:27382569:A:T	C63S	0.867
1:27382577:C:G	C60S	0.864
1:27382578:A:T	C60S	0.864
1:27382577:C:T	C60Y	0.859
1:27382333:C:G	C108S	0.855
1:27382334:A:T	C108S	0.855
1:27382532:C:G	C75S	0.847
1:27382533:A:T	C75S	0.847

dbSNP variants (sampled 300 via entrez): RS1000690253 (1:27381640 C>A,G), RS1001135366 (1:27384185 A>T), RS1002194981 (1:27385119 T>G), RS1002272046 (1:27378751 G>A), RS1002323172 (1:27383019 A>C,G), RS1003207847 (1:27383647 G>A,T), RS1004242377 (1:27382284 G>A), RS1004318961 (1:27380126 A>G), RS1004351387 (1:27379675 C>G,T), RS1006250805 (1:27383098 T>G), RS1007012222 (1:27384084 A>G), RS1007043238 (1:27383727 C>T), RS1008014760 (1:27382999 G>C), RS1008566874 (1:27379033 C>T), RS1008645052 (1:27380489 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

1 associations (top):

Study	Trait	p-value
GCST008479_18	Psoriasis	6.000000e-06

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
Air Pollutants	increases abundance, increases expression, decreases expression	2
tobacco tar	decreases expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	affects cotreatment, increases expression	1
ICG 001	increases expression	1
Decitabine	decreases methylation	1
Benzo(a)pyrene	decreases methylation	1
Camptothecin	increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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