CHODL

Summary

CHODL (chondrolectin, HGNC:17807) is a protein-coding gene on chromosome 21q21.1, encoding Chondrolectin (Q9H9P2). May play a role in the development of the nervous system such as in neurite outgrowth and elongation.

This gene encodes a type I membrane protein with a carbohydrate recognition domain characteristic of C-type lectins in its extracellular portion. In other proteins, this domain is involved in endocytosis of glycoproteins and exogenous sugar-bearing pathogens. This protein localizes predominantly to the perinuclear region. Several transcript variants encoding a few different isoforms have been found for this gene.

Source: NCBI Gene 140578 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_024944

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17807
Approved symbol	CHODL
Name	chondrolectin
Location	21q21.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12627, PRED12, MT75
Ensembl gene	ENSG00000154645
Ensembl biotype	protein_coding
OMIM	607247
Entrez	140578

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000299295, ENST00000338326, ENST00000400127, ENST00000400128, ENST00000400131, ENST00000400135, ENST00000543733

RefSeq mRNA: 6 — MANE Select: NM_024944 NM_001204174, NM_001204175, NM_001204176, NM_001204177, NM_001204178, NM_024944

CCDS: CCDS13570, CCDS56208, CCDS56209, CCDS56210

Canonical transcript exons

ENST00000299295 — 6 exons

Exon	Start	End
ENSE00001016988	18262791	18262893
ENSE00001016989	18260200	18260286
ENSE00001016990	18256970	18257127
ENSE00003468151	18244833	18245302
ENSE00003659737	18256509	18256818
ENSE00003845563	18265954	18267370

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 98.55.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1031 / max 148.8580, expressed in 201 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
188591	1.0583	181
188588	0.0448	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.55	gold quality
right testis	UBERON:0004534	89.15	gold quality
left testis	UBERON:0004533	87.52	gold quality
testis	UBERON:0000473	86.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.13	gold quality
adult organism	UBERON:0007023	78.66	gold quality
tendon	UBERON:0000043	77.74	gold quality
colonic epithelium	UBERON:0000397	72.96	gold quality
spleen	UBERON:0002106	72.72	gold quality
hypothalamus	UBERON:0001898	72.42	gold quality
rectum	UBERON:0001052	71.77	gold quality
inferior olivary complex	UBERON:0002127	70.99	gold quality
ganglionic eminence	UBERON:0004023	69.71	gold quality
right atrium auricular region	UBERON:0006631	69.62	gold quality
mucosa of stomach	UBERON:0001199	69.44	gold quality
hair follicle	UBERON:0002073	69.34	gold quality
metanephros cortex	UBERON:0010533	68.60	gold quality
cardiac atrium	UBERON:0002081	68.34	gold quality
decidua	UBERON:0002450	68.04	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	67.94	silver quality
omental fat pad	UBERON:0010414	67.87	gold quality
tibial artery	UBERON:0007610	67.84	gold quality
popliteal artery	UBERON:0002250	67.80	gold quality
peritoneum	UBERON:0002358	67.79	gold quality
descending thoracic aorta	UBERON:0002345	67.72	gold quality
ventricular zone	UBERON:0003053	67.41	gold quality
muscle layer of sigmoid colon	UBERON:0035805	66.69	gold quality
aorta	UBERON:0000947	66.67	gold quality
adipose tissue of abdominal region	UBERON:0007808	66.61	gold quality
lower esophagus muscularis layer	UBERON:0035833	66.48	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-8221	yes	432.66
E-ANND-3	no	3.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting CHODL, 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-3646	100.00	73.56	5283
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548P	99.98	72.25	3784
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-507	99.97	70.11	1915
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-590-3P	99.96	74.34	6478
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6844	99.82	70.69	2423

Literature-anchored findings (GeneRIF, showing 4)

• cloning and characterization; localized at chromosome 21q21 (PMID:12079284)
• study describes the molecular characterization of novel members of the chondrolectin family associated with T cell maturation and a subcellular localization of chondrolectin f isoform in the endoplasmic reticulum-Golgi apparatus (PMID:12621022)
• CHODLDeltaE/CHODLfDeltaE protein variant localizes in the late endoplasmic reticulum and is detected in spleen and tonsils; the isoform seems to be differentially expressed in thymocytes and lymphocytes. (PMID:17606388)
• Data indicate that chondrolectin (CHODL) is likely to be a prognostic biomarker in the clinic and targeting CHODL might be a strategy for the development of anticancer drugs. (PMID:22016508)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	chodl	ENSDARG00000034528
mus_musculus	Chodl	ENSMUSG00000022860
rattus_norvegicus	Chodl	ENSRNOG00000001915

Paralogs (1): LAYN (ENSG00000204381)

Protein

Protein identifiers

Chondrolectin — Q9H9P2 (reviewed: Q9H9P2)

Alternative names: Transmembrane protein MT75

All UniProt accessions (2): Q9H9P2, A0A0C4DFS2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the development of the nervous system such as in neurite outgrowth and elongation. May be involved in motor axon growth and guidance.

Subunit / interactions. Interacts with RABGGTB.

Subcellular location. Cytoplasm. Membrane Endoplasmic reticulum. Endoplasmic reticulum membrane Cytoplasm.

Tissue specificity. Found in spleen, testis, prostate and fetal liver. Expression limited to vascular muscle of testis, smooth muscle of prostate stroma, heart muscle, skeletal muscle, crypts of small intestine, and red pulp of spleen. B lymphocytes express isoform 2 only; peripheral blood T lymphocytes express isoform 3 only; granulocytes and monocytes express neither isoform 2 nor isoform 3. During development of T lymphocytes, bone marrow progenitor cells express isoform 2 only; thymocytes at different stages of maturation express predominantly isoform 2 and weakly isoform 3, and mature thymocytes express only isoform 2.

Post-translational modifications. N-glycosylated.

Miscellaneous. A protein of the expected size has been detected by antibody binding and Western blot in at least one of the analyzed tissues or cells. Produced by alternative promoter usage. Produced by alternative promoter usage. Produced by alternative splicing of isoform 2. Produced by alternative splicing of isoform 1.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9H9P2-1	1	yes
Q9H9P2-2	2, CHODLF
Q9H9P2-3	3, CHODLFdeltaE
Q9H9P2-4	4

RefSeq proteins (6): NP_001191103, NP_001191104, NP_001191105, NP_001191106, NP_001191107, NP_079220* (*=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
IPR051505	C-type_lectin_domain	Family

Pfam: PF00059

UniProt features (16 total): splice variant 3, disulfide bond 2, sequence conflict 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H9P2-F1	76.83	0.47

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): 144–170, 61–178

Glycosylation sites (1): 86

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, BENPORATH_ES_WITH_H3K27ME3, GOBP_NEUROGENESIS, MAHADEVAN_IMATINIB_RESISTANCE_DN, CERVERA_SDHB_TARGETS_1_DN, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GTGCCTT_MIR506, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, TGIF_01, GOMF_GLYCOSAMINOGLYCAN_BINDING, AACTTT_UNKNOWN, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT

GO Biological Process (4): nervous system development (GO:0007399), muscle organ development (GO:0007517), positive regulation of axonogenesis (GO:0050772), regulation of neuron projection development (GO:0010975)

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

GO Cellular Component (7): cytoplasm (GO:0005737), endoplasmic reticulum membrane (GO:0005789), centrosome (GO:0005813), cytosol (GO:0005829), perinuclear region of cytoplasm (GO:0048471), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cytoplasm	3
binding	2
system development	1
animal organ development	1
muscle structure development	1
axonogenesis	1
positive regulation of cell projection organization	1
positive regulation of neurogenesis	1
regulation of axonogenesis	1
neuron projection development	1
regulation of plasma membrane bounded cell projection organization	1
intracellular anatomical structure	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
centriole	1
microtubule organizing center	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

758 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHODL	LAMP5	Q9UJQ1	558
CHODL	TMEM41B	Q5BJD5	523
CHODL	PCDH20	Q8N6Y1	473
CHODL	VIPR2	P41587	472
CHODL	BTG3	Q14201	467
CHODL	TMPRSS15	P98073	436
CHODL	CBLN4	Q9NTU7	431
CHODL	NCAM2	O15394	422
CHODL	TRARG1	Q8IXB3	409
CHODL	VSTM2B	A6NLU5	407
CHODL	SNCG	O76070	407
CHODL	XIRP1	Q702N8	389
CHODL	APOE	P02649	385
CHODL	PARPBP	Q9NWS1	373
CHODL	FBLN2	P98095	372

IntAct

32 interactions, top by confidence:

A	B	Type	Score
ZDHHC21	CHODL	psi-mi:“MI:0915”(physical association)	0.560
BNIP2	CHODL	psi-mi:“MI:0915”(physical association)	0.560
CXCL9	CHODL	psi-mi:“MI:0915”(physical association)	0.560
IGFBP5	CHODL	psi-mi:“MI:0915”(physical association)	0.560
CHODL	DOLK	psi-mi:“MI:0915”(physical association)	0.560
CHODL	NINJ2	psi-mi:“MI:0915”(physical association)	0.560
BCL2L2	CHODL	psi-mi:“MI:0915”(physical association)	0.560
SCGB1D1	CHODL	psi-mi:“MI:0915”(physical association)	0.560
C2CD2L	CHODL	psi-mi:“MI:0915”(physical association)	0.560
EBP	CHODL	psi-mi:“MI:0915”(physical association)	0.560
CHODL	RAD51C	psi-mi:“MI:0914”(association)	0.350
IGFBP5	CHODL	psi-mi:“MI:0915”(physical association)	0.000
DOLK	CHODL	psi-mi:“MI:0915”(physical association)	0.000
NINJ2	CHODL	psi-mi:“MI:0915”(physical association)	0.000
BCL2L2	CHODL	psi-mi:“MI:0915”(physical association)	0.000
BNIP2	CHODL	psi-mi:“MI:0915”(physical association)	0.000
CXCL9	CHODL	psi-mi:“MI:0915”(physical association)	0.000
SCGB1D1	CHODL	psi-mi:“MI:0915”(physical association)	0.000
C2CD2L	CHODL	psi-mi:“MI:0915”(physical association)	0.000
EBP	CHODL	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (32): CHODL (Two-hybrid), CHODL (Two-hybrid), CHODL (Two-hybrid), CHODL (Two-hybrid), CHODL (Two-hybrid), SCGB1D1 (Two-hybrid), NINJ2 (Two-hybrid), C2CD2L (Two-hybrid), DOLK (Two-hybrid), ZDHHC21 (Two-hybrid), TTK (Affinity Capture-MS), MDN1 (Affinity Capture-MS), COL2A1 (Affinity Capture-MS), EIF2B4 (Affinity Capture-MS), SGPL1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNA2, A2RRU4, A4FUY1, A5D7V5, A8MVS5, D4A6L0, E1BBQ2, O19131, O54693, O75144, P09564, P15151, P19438, P29590, P31994, P32506, P32507, P50555, P97260, Q14CZ8, Q28110, Q3TEW6, Q53EL9, Q5BJT4, Q5DRQ8, Q5T848, Q61190, Q640R3, Q6AYP5, Q6AYT8, Q6BAA4, Q6GQT6, Q6P6J9, Q6UX15, Q70EL4, Q75VT8, Q7TSK2, Q7Z692, Q8C419, Q8N126

Diamond homologs: Q568T5, Q6UX15, Q8C351, Q9CXM0, Q9H9P2, Q9Z209, P06734, P22897, Q4TU93, Q4V885, Q64449, Q8CJ91, Q8HY06, Q8HY10, Q8HY11, Q8HY12, Q8HYC0, Q8K4Q8, Q91ZW8, Q9UBG0, P13611, P81282, P84615, Q5KU26, Q7LZK5, Q7TSQ1, A0ZT93, B4XSY5, B4XSY6, B4XT01, B4XT02, B4XT03, B4XT08, C0HKZ7, D2YVH7, D2YVI2, D2YVJ8, D2YVK5, D2YW40, D3ZTE0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

792 predictions. Top by Δscore:

Variant	Effect	Δscore
21:18245300:GCG:G	donor_gain	1.0000
21:18256818:GGTG:G	donor_loss	1.0000
21:18256819:G:GG	donor_gain	1.0000
21:18256820:T:G	donor_loss	1.0000
21:18256961:T:A	acceptor_gain	1.0000
21:18256966:GCA:G	acceptor_loss	1.0000
21:18256968:A:AG	acceptor_gain	1.0000
21:18256969:G:GG	acceptor_gain	1.0000
21:18256969:GA:G	acceptor_gain	1.0000
21:18256969:GAA:G	acceptor_gain	1.0000
21:18256969:GAAA:G	acceptor_gain	1.0000
21:18256969:GAAAC:G	acceptor_gain	1.0000
21:18257126:AG:A	donor_loss	1.0000
21:18257127:GG:G	donor_loss	1.0000
21:18260196:ACAG:A	acceptor_loss	1.0000
21:18260198:A:AG	acceptor_gain	1.0000
21:18260198:A:C	acceptor_loss	1.0000
21:18260199:G:GG	acceptor_gain	1.0000
21:18260199:GA:G	acceptor_gain	1.0000
21:18260199:GAGA:G	acceptor_gain	1.0000
21:18260199:GAGAT:G	acceptor_gain	1.0000
21:18265952:A:AG	acceptor_gain	1.0000
21:18265953:G:GA	acceptor_gain	1.0000
21:18265953:GTA:G	acceptor_gain	1.0000
21:18265953:GTAAA:G	acceptor_gain	1.0000
21:18245299:AGCGG:A	donor_loss	0.9900
21:18245301:CGGTG:C	donor_loss	0.9900
21:18245302:GGT:G	donor_loss	0.9900
21:18245303:G:GG	donor_gain	0.9900
21:18245303:GTGA:G	donor_loss	0.9900

AlphaMissense

1798 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:18256611:G:A	C61Y	1.000
21:18256727:T:A	W100R	1.000
21:18256727:T:C	W100R	1.000
21:18256729:G:C	W100C	1.000
21:18256729:G:T	W100C	1.000
21:18256792:G:C	W121C	1.000
21:18256792:G:T	W121C	1.000
21:18256974:T:A	W132R	1.000
21:18256974:T:C	W132R	1.000
21:18256976:G:C	W132C	1.000
21:18256976:G:T	W132C	1.000
21:18256987:A:T	E136V	1.000
21:18256989:C:T	P137S	1.000
21:18256990:C:A	P137H	1.000
21:18257005:A:T	E142V	1.000
21:18257010:T:A	C144S	1.000
21:18257010:T:C	C144R	1.000
21:18257011:G:C	C144S	1.000
21:18257012:T:G	C144W	1.000
21:18257023:A:G	Y148C	1.000
21:18257073:T:A	W165R	1.000
21:18257073:T:C	W165R	1.000
21:18257074:G:C	W165S	1.000
21:18257075:G:C	W165C	1.000
21:18257075:G:T	W165C	1.000
21:18257078:T:A	N166K	1.000
21:18257078:T:G	N166K	1.000
21:18257079:G:C	D167H	1.000
21:18257079:G:T	D167Y	1.000
21:18257080:A:C	D167A	1.000

dbSNP variants (sampled 300 via entrez): RS1000009022 (21:18137442 A>G), RS1000011487 (21:17958880 C>G,T), RS1000015472 (21:18232240 T>C), RS1000019997 (21:18119849 G>T), RS1000025080 (21:18008383 T>C), RS1000031128 (21:18225712 A>C,G), RS1000037388 (21:18059969 A>T), RS1000039725 (21:18218550 G>A), RS1000046996 (21:18213814 C>A), RS1000051422 (21:18056790 T>C), RS1000057189 (21:17921058 G>A,T), RS1000066516 (21:18184518 A>C), RS1000071625 (21:18235054 A>G), RS1000079251 (21:17997838 GAGATAC>G), RS1000079388 (21:18158566 G>A,C)

Disease associations

OMIM: gene MIM:607247 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST001958_21	Bulimia nervosa	1.000000e-06
GCST002005_2	Adverse response to chemotherapy (neutropenia/leucopenia) (all antimetabolite drugs)	9.000000e-06
GCST002337_27	Amyotrophic lateral sclerosis (sporadic)	6.000000e-06
GCST004864_4	Perceived unattractiveness to mosquitoes	4.000000e-06
GCST010152_9	Neuroblastoma or malignant cutaneous melanoma	7.000000e-07
GCST012116_4	Rheumatic heart disease	5.000000e-06
GCST012490_316	Femur bone mineral density x serum urate levels interaction	2.000000e-09
GCST012490_590	Femur bone mineral density x serum urate levels interaction	1.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008380	perceived unattractiveness to mosquitos measurement
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, decreases expression, affects cotreatment	5
mercuric bromide	affects cotreatment, increases expression	2
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
bisphenol A	increases methylation, affects cotreatment	1
testosterone undecanoate	decreases expression	1
trichostatin A	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	decreases methylation, affects cotreatment	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation, decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Copper	decreases expression, affects cotreatment	1
Doxorubicin	increases expression	1
Endosulfan	increases expression	1
Folic Acid	decreases expression	1
Nickel	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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