CDR2L

Summary

CDR2L (cerebellar degeneration related protein 2 like, HGNC:29999) is a protein-coding gene on chromosome 17q25.1, encoding Cerebellar degeneration-related protein 2-like (Q86X02).

Enables identical protein binding activity. Predicted to be involved in Golgi to secretory granule transport and vesicle transport along microtubule. Predicted to be located in cytoplasm.

Source: NCBI Gene 30850 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_014603

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29999
Approved symbol	CDR2L
Name	cerebellar degeneration related protein 2 like
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Aliases	HUMPPA
Ensembl gene	ENSG00000109089
Ensembl biotype	protein_coding
Entrez	30850

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000337231, ENST00000909937

RefSeq mRNA: 1 — MANE Select: NM_014603 NM_014603

CCDS: CCDS11710

Canonical transcript exons

ENST00000337231 — 5 exons

Exon	Start	End
ENSE00001058397	74999504	74999616
ENSE00001117762	75001341	75001489
ENSE00001117763	75002064	75002228
ENSE00001342862	74987632	74988122
ENSE00001925443	75003183	75005800

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 94.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.2264 / max 341.5152, expressed in 1586 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
162683	24.2264	1586

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
inferior vagus X ganglion	UBERON:0005363	94.40	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.08	gold quality
cerebellar hemisphere	UBERON:0002245	92.94	gold quality
cerebellar cortex	UBERON:0002129	92.90	gold quality
cerebellum	UBERON:0002037	92.05	gold quality
decidua	UBERON:0002450	91.80	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.74	gold quality
spinal cord	UBERON:0002240	91.03	gold quality
dorsal root ganglion	UBERON:0000044	89.22	gold quality
stromal cell of endometrium	CL:0002255	88.92	gold quality
pons	UBERON:0000988	88.31	gold quality
medulla oblongata	UBERON:0001896	87.98	gold quality
subthalamic nucleus	UBERON:0001906	87.78	gold quality
ventral tegmental area	UBERON:0002691	87.38	gold quality
superior vestibular nucleus	UBERON:0007227	87.27	gold quality
pylorus	UBERON:0001166	86.79	gold quality
dorsal plus ventral thalamus	UBERON:0001897	86.77	gold quality
lateral nuclear group of thalamus	UBERON:0002736	86.44	gold quality
cerebellar vermis	UBERON:0004720	86.33	gold quality
apex of heart	UBERON:0002098	86.12	gold quality
vena cava	UBERON:0004087	86.07	silver quality
midbrain	UBERON:0001891	85.74	gold quality
cardia of stomach	UBERON:0001162	85.51	gold quality
substantia nigra	UBERON:0002038	85.26	gold quality
duodenum	UBERON:0002114	84.83	gold quality
heart left ventricle	UBERON:0002084	84.11	gold quality
inferior olivary complex	UBERON:0002127	84.07	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	84.06	gold quality
cardiac ventricle	UBERON:0002082	83.94	gold quality
pancreatic ductal cell	CL:0002079	83.65	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7051	yes	1875.73
E-ANND-3	yes	7.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

143 targeting CDR2L, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-1297	99.91	73.41	3162

Literature-anchored findings (GeneRIF, showing 4)

• Both cerebellar degeneration related protein 2 (CDR2) and cerebellar degeneration-related antigen CDR2L (CDR2L) are more widely expressed than previously thought, both in normal and cancerous tissues. (PMID:28710511)
• Paraneoplastic cerebellar degenerations with anti-Yo antibodies (Yo-PCD) tumors differed from the 116 control tumors by more abundant T and B cells infiltration occasionally organized in tertiary lymphoid structures harboring CDR2L protein deposits. 65% of Yo-PCD tumors cohort presented at least one somatic mutation in CDR2 and CDR2L with a predominance of missense mutations. (PMID:29299667)
• Paraneoplastic Cerebellar Degeneration: The Importance of Including CDR2L as a Diagnostic Marker. (PMID:33531379)
• A cerebellar degeneration-related protein 2-like cell-based assay for anti-Yo detection in patients with paraneoplastic cerebellar degeneration. (PMID:36912432)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdr2l	ENSDARG00000026834
mus_musculus	Cdr2l	ENSMUSG00000050910
rattus_norvegicus	Cdr2l	ENSRNOG00000025815
drosophila_melanogaster	Cen	FBGN0032876

Paralogs (1): CDR2 (ENSG00000140743)

Protein

Protein identifiers

Cerebellar degeneration-related protein 2-like — Q86X02 (reviewed: Q86X02)

Alternative names: Paraneoplastic 62 kDa antigen

All UniProt accessions (1): Q86X02

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CDR2 family.

RefSeq proteins (1): NP_055418* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026079	CDR2	Family

UniProt features (12 total): coiled-coil region 3, modified residue 3, region of interest 2, chain 1, sequence variant 1, sequence conflict 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86X02-F1	74.27	0.46

Functional residue map

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

Post-translational modifications (3): 308, 318, 344

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 149 (showing top): GGGACCA_MIR133A_MIR133B, GOBP_VESICLE_LOCALIZATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, GGGTGGRR_PAX4_03, GOBP_VESICLE_CYTOSKELETAL_TRAFFICKING, BLALOCK_ALZHEIMERS_DISEASE_UP, CAATGCA_MIR33, TGACATY_UNKNOWN, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, MODULE_88, AACTTT_UNKNOWN, BROWNE_HCMV_INFECTION_6HR_UP, BROWNE_HCMV_INFECTION_10HR_UP

GO Biological Process (2): vesicle transport along microtubule (GO:0047496), Golgi to secretory granule transport (GO:0055107)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
organelle transport along microtubule	1
vesicle cytoskeletal trafficking	1
intercellular transport	1
intracellular transport	1
protein binding	1
binding	1

Protein interactions and networks

STRING

348 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDR2L	ZCCHC12	Q6PEW1	952
CDR2L	PNMA5	Q96PV4	544
CDR2L	DPYSL5	Q9BPU6	511
CDR2L	PNMA6F	A0A0J9YX94	507
CDR2L	CUEDC1	Q9NWM3	507
CDR2L	HOMER3	Q9NSC5	478
CDR2L	DNER	Q8NFT8	477
CDR2L	CDC42SE2	Q9NRR3	476
CDR2L	PNMA2	Q9UL42	473
CDR2L	BIN1	O00499	459
CDR2L	RPS6	P08227	459
CDR2L	PNMA6A	P0CW24	445
CDR2L	SOX14	O95416	426
CDR2L	MS4A6A	Q9H2W1	422
CDR2L	ARHGAP26	Q9UNA1	421

IntAct

246 interactions, top by confidence:

A	B	Type	Score
CDR2	CDR2L	psi-mi:“MI:0915”(physical association)	0.880
BFSP2	CDR2L	psi-mi:“MI:0915”(physical association)	0.800
CDR2	KTN1	psi-mi:“MI:0914”(association)	0.730
C4orf46	CDR2L	psi-mi:“MI:0915”(physical association)	0.670
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
CDR2L	CDR2L	psi-mi:“MI:0915”(physical association)	0.600
CDR2L		psi-mi:“MI:0915”(physical association)	0.560
CDR2L	UBE2I	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	ZNF19	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	TCP10L	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	FAM86C1P	psi-mi:“MI:0915”(physical association)	0.560
EHHADH	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
ZNF80	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
REL	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
ZNF572	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	RASD1	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	MGC50722	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	INO80B	psi-mi:“MI:0915”(physical association)	0.560
ZNF250	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
STX11	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
TSGA10IP	CDR2L	psi-mi:“MI:0915”(physical association)	0.560
COX5B	CDR2L	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (143): CDR2L (Affinity Capture-MS), CDR2L (Affinity Capture-MS), CDR2L (Affinity Capture-MS), CDR2L (Affinity Capture-MS), CDR2L (Affinity Capture-MS), CDR2 (Affinity Capture-MS), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid), CDR2L (Two-hybrid)

ESM2 similar proteins: A0A8I3QA39, A1YB07, A2A6T1, A2A9T0, A2AHG0, A5PKL7, A6NKD9, A7MCY6, B8A5S6, D3ZD05, E1BEQ5, E1U8D0, E9Q6B2, F1MRK3, G3V735, O14529, O60299, O75145, O94964, P60469, Q1LZH7, Q3LUD4, Q3UIL6, Q499E4, Q5JTD0, Q5RCR6, Q5XIA0, Q62036, Q63ZY3, Q6DG50, Q6IQ23, Q6NZT2, Q6PDH0, Q86UU1, Q86X02, Q8BX02, Q8C7U1, Q8IY63, Q8K1Q4, Q8K371

Diamond homologs: A2A6T1, P97817, Q01850, Q5ZJA3, Q6NZT2, Q86X02

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	67
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

726 predictions. Top by Δscore:

Variant	Effect	Δscore
17:74999497:A:AG	acceptor_gain	1.0000
17:74999502:A:AG	acceptor_gain	1.0000
17:74999502:A:G	acceptor_loss	1.0000
17:74999503:G:GC	acceptor_gain	1.0000
17:74999503:GA:G	acceptor_gain	1.0000
17:74999503:GAC:G	acceptor_gain	1.0000
17:74999503:GACT:G	acceptor_gain	1.0000
17:74999503:GACTT:G	acceptor_gain	1.0000
17:74999613:CGAG:C	donor_loss	1.0000
17:74999614:GAGG:G	donor_loss	1.0000
17:74999615:AG:A	donor_loss	1.0000
17:74999618:T:G	donor_loss	1.0000
17:75001333:A:AG	acceptor_gain	1.0000
17:75001334:C:G	acceptor_gain	1.0000
17:75001337:CCA:C	acceptor_loss	1.0000
17:75001339:A:AG	acceptor_gain	1.0000
17:75001339:A:C	acceptor_loss	1.0000
17:75001340:G:GT	acceptor_gain	1.0000
17:75001340:GT:G	acceptor_gain	1.0000
17:75001340:GTA:G	acceptor_gain	1.0000
17:75001340:GTAC:G	acceptor_gain	1.0000
17:75001340:GTACC:G	acceptor_gain	1.0000
17:75001457:GGAGA:G	donor_gain	1.0000
17:75001458:GAGA:G	donor_gain	1.0000
17:75001458:GAGAG:G	donor_gain	1.0000
17:75001459:A:T	donor_gain	1.0000
17:75001460:GA:G	donor_gain	1.0000
17:75001462:G:GG	donor_gain	1.0000
17:75001488:GG:G	donor_gain	1.0000
17:75001489:GG:G	donor_gain	1.0000

AlphaMissense

3007 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:75003982:T:C	Y436H	1.000
17:75003994:T:C	F440L	1.000
17:75003996:C:A	F440L	1.000
17:75003996:C:G	F440L	1.000
17:75001345:T:C	L66P	0.999
17:75003754:T:G	Y360D	0.999
17:75003764:T:C	L363P	0.999
17:75003785:T:C	L370P	0.999
17:75003983:A:G	Y436C	0.999
17:75003987:G:C	K437N	0.999
17:75003987:G:T	K437N	0.999
17:75003992:T:C	L439P	0.999
17:75003994:T:G	F440V	0.999
17:75003995:T:C	F440S	0.999
17:75003995:T:G	F440C	0.999
17:75004004:T:C	I443T	0.999
17:75004004:T:G	I443S	0.999
17:75004006:T:C	F444L	0.999
17:75004008:C:A	F444L	0.999
17:75004008:C:G	F444L	0.999
17:75004016:T:C	I447T	0.999
17:74999527:G:A	G35R	0.998
17:74999527:G:C	G35R	0.998
17:75003734:T:C	L353P	0.998
17:75003754:T:C	Y360H	0.998
17:75003982:T:G	Y436D	0.998
17:75003983:A:C	Y436S	0.998
17:75003992:T:A	L439H	0.998
17:75003994:T:A	F440I	0.998
17:75004004:T:A	I443N	0.998

dbSNP variants (sampled 300 via entrez): RS1000034106 (17:75000764 A>G), RS1000064187 (17:74993810 A>G,T), RS1000504340 (17:74987739 A>C), RS1000639773 (17:74999299 CACACACACACACACACAG>C), RS1000741258 (17:75005506 C>A,G), RS1000785486 (17:74992695 A>C), RS1000833768 (17:74988372 C>A,T), RS1000890308 (17:75006276 G>A), RS1001011822 (17:74999034 T>C), RS1001046723 (17:74985866 C>A), RS1001063986 (17:74992206 T>G), RS1001103577 (17:74994486 T>C), RS1001202206 (17:74987035 GT>G,GTT), RS1001367379 (17:74987689 G>A,C), RS1001378888 (17:74987962 C>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

2 associations (top):

Study	Trait	p-value
GCST002817_15	Alzheimer’s disease in APOE e4- carriers	9.000000e-07
GCST008103_113	Bipolar disorder	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	4
Aflatoxin B1	affects expression, increases expression, increases methylation	3
Cyclosporine	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
methylmercuric chloride	increases expression	1
methyleugenol	increases expression	1
bisphenol A	decreases methylation	1
sodium arsenate	increases expression, increases abundance	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
coumarin	increases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
beta-methylcholine	affects expression	1
pentanal	increases expression	1
Am 580	decreases expression	1
ICG 001	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Rosiglitazone	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Atrazine	increases expression	1
Calcitriol	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression, affects cotreatment	1
Methapyrilene	decreases methylation	1
N-Nitrosopyrrolidine	increases expression	1
Quercetin	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E1AE	Ubigene OVCAR-3 CDR2L KO	Cancer cell line	Female

Clinical trials (associated diseases)

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