YDJC

Summary

YDJC (YdjC chitooligosaccharide deacetylase homolog, HGNC:27158) is a protein-coding gene on chromosome 22q11.21, encoding Carbohydrate deacetylase (A8MPS7). Probably catalyzes the deacetylation of acetylated carbohydrates an important step in the degradation of oligosaccharides.

Predicted to enable deacetylase activity and magnesium ion binding activity. Predicted to be involved in carbohydrate metabolic process.

Source: NCBI Gene 150223 — RefSeq curated summary.

At a glance

• GWAS associations: 23
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_001017964

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27158
Approved symbol	YDJC
Name	YdjC chitooligosaccharide deacetylase homolog
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000161179
Ensembl biotype	protein_coding
OMIM	619770
Entrez	150223

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000292778, ENST00000398873, ENST00000415762, ENST00000464015, ENST00000468686, ENST00000473985, ENST00000482998, ENST00000916138, ENST00000916139, ENST00000953638

RefSeq mRNA: 2 — MANE Select: NM_001017964 NM_001017964, NM_001371350

CCDS: CCDS33613, CCDS93126

Canonical transcript exons

ENST00000292778 — 5 exons

Exon	Start	End
ENSE00003509849	21629308	21629407
ENSE00003630670	21629010	21629187
ENSE00003677110	21629602	21629761
ENSE00003683671	21628089	21628787
ENSE00003897997	21629851	21630022

Expression profiles

Bgee: expression breadth ubiquitous, 177 present calls, max score 93.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.6591 / max 920.8314, expressed in 1798 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193233	44.9573	1797
193232	1.7017	589

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	93.54	gold quality
granulocyte	CL:0000094	89.62	gold quality
mucosa of transverse colon	UBERON:0004991	89.60	gold quality
pancreatic ductal cell	CL:0002079	88.89	silver quality
right uterine tube	UBERON:0001302	88.08	gold quality
lower esophagus mucosa	UBERON:0035834	86.27	gold quality
body of pancreas	UBERON:0001150	85.98	gold quality
metanephros cortex	UBERON:0010533	85.70	gold quality
spleen	UBERON:0002106	85.44	gold quality
left lobe of thyroid gland	UBERON:0001120	85.08	gold quality
esophagus mucosa	UBERON:0002469	85.01	gold quality
right lobe of thyroid gland	UBERON:0001119	84.82	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.44	gold quality
adult mammalian kidney	UBERON:0000082	84.40	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.26	gold quality
skin of abdomen	UBERON:0001416	84.14	gold quality
right lobe of liver	UBERON:0001114	84.11	gold quality
anterior cingulate cortex	UBERON:0009835	83.86	gold quality
skin of leg	UBERON:0001511	83.84	gold quality
right frontal lobe	UBERON:0002810	83.66	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.63	gold quality
body of stomach	UBERON:0001161	83.52	gold quality
metanephros	UBERON:0000081	83.45	gold quality
thyroid gland	UBERON:0002046	83.39	gold quality
leukocyte	CL:0000738	83.37	gold quality
transverse colon	UBERON:0001157	83.32	gold quality
upper arm skin	UBERON:0004263	83.24	gold quality
cortex of kidney	UBERON:0001225	83.19	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.10	gold quality
monocyte	CL:0000576	83.05	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.61
E-MTAB-6379	no	307.88
E-GEOD-36552	no	62.91
E-CURD-112	no	3.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting YDJC, 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-6764-5P	99.75	67.89	2304
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-421	98.90	67.04	1883
HSA-MIR-4473	98.89	69.10	652
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-4751	98.80	64.95	525
HSA-MIR-4450	98.26	68.35	725
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-6515-5P	97.08	65.48	1219
HSA-MIR-1913	97.07	66.20	1417

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ydjc	ENSDARG00000062655
mus_musculus	Ydjc	ENSMUSG00000041774
rattus_norvegicus	Ydjc	ENSRNOG00000001861

Protein

Protein identifiers

Carbohydrate deacetylase — A8MPS7 (reviewed: A8MPS7)

All UniProt accessions (1): A8MPS7

UniProt curated annotations — full annotation on UniProt →

Function. Probably catalyzes the deacetylation of acetylated carbohydrates an important step in the degradation of oligosaccharides.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the YdjC deacetylase family.

Isoforms (3)

UniProt ID	Names	Canonical?
A8MPS7-1	1	yes
A8MPS7-2	2
A8MPS7-3	3

RefSeq proteins (2): NP_001017964, NP_001358279 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006879	YdjC-like	Family
IPR011330	Glyco_hydro/deAcase_b/a-brl	Homologous_superfamily

Pfam: PF04794

Enzyme classification (BRENDA):

• EC 3.5.1.105 — chitin disaccharide deacetylase (BRENDA: 21 organisms, 52 substrates, 9 inhibitors, 9 Km, 3 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
N,N’-DIACETYLCHITOBIOSE	0.83–7.04	5
GLCNAC-BETA-(1,4)-GLCNAC	0.24–1.93	2
2-(ACETYLAMINO)-4-O-[2-(ACETYLAMINO)-2-DEOXY-BET	31.8	1
GLCNAC-BETA-1,4-GLCNAC-BETA-1,4-GLCNAC	98	1

UniProt features (9 total): splice variant 4, binding site 2, chain 1, active site 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MPS7-F1	91.77	0.86

Functional residue map

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

Catalytic / active sites (1): 13 (proton acceptor)

Ligand- & substrate-binding residues (2): 14; 134

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): CACCAGC_MIR138, TTGGGAG_MIR150, WEI_MYCN_TARGETS_WITH_E_BOX, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, LIU_SOX4_TARGETS_DN, GOMF_MAGNESIUM_ION_BINDING, GOMF_DEACETYLASE_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3K4ME2, MARTENS_TRETINOIN_RESPONSE_DN, LEE_BMP2_TARGETS_DN, VANLOO_SP3_TARGETS_DN, STK33_SKM_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_DN

GO Biological Process (1): carbohydrate metabolic process (GO:0005975)

GO Molecular Function (4): magnesium ion binding (GO:0000287), hydrolase activity (GO:0016787), deacetylase activity (GO:0019213), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
metal ion binding	1
catalytic activity	1
deacylase activity	1
cation binding	1

Protein interactions and networks

STRING

406 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
YDJC	ZMIZ1	Q9ULJ6	514
YDJC	CCDC116	Q8IYX3	464
YDJC	CDC16	Q13042	463
YDJC	H7C0V5	H7C0V5	432
YDJC	RIMBP3B	A6NNM3	399
YDJC	EMP2	P54851	387
YDJC	ZNF623	O75123	376
YDJC	B9ZVM9	B9ZVM9	371
YDJC	ZHX1-C8orf76	Q96EF9	370
YDJC	POP1	Q99575	370
YDJC	NUDT8	Q8WV74	369
YDJC	C8orf76	Q96K31	366
YDJC	WDR47	O94967	359
YDJC	TIGD5	Q53EQ6	357
YDJC	DCAF1	Q9Y4B6	354

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CDC16	IFT56	psi-mi:“MI:0914”(association)	0.350
PCMT1	YDJC	psi-mi:“MI:0914”(association)	0.350
ARSG	YDJC	psi-mi:“MI:0914”(association)	0.350

BioGRID (22): YDJC (Affinity Capture-RNA), YDJC (Affinity Capture-MS), YDJC (Affinity Capture-MS), YDJC (Affinity Capture-MS), YDJC (Affinity Capture-MS), PPP2CA (Affinity Capture-Western), YDJC (Affinity Capture-MS), YDJC (Affinity Capture-MS), YDJC (Affinity Capture-MS), YDJC (Proximity Label-MS), YDJC (Proximity Label-MS), YDJC (Proximity Label-MS), YDJC (Proximity Label-MS), YDJC (Proximity Label-MS), YDJC (Proximity Label-MS)

ESM2 similar proteins: A2XFU4, A2XFU5, A2XVN3, A2YQ58, A3AVP1, A4D2B0, A4IFA8, A7HDG9, A8ID74, A8IF44, A8J1V4, A8MPS7, B1WBV0, B4UH39, B8JE35, G8XHD8, O86507, P29784, P52824, Q08325, Q0D3F2, Q0D9V6, Q0DSH9, Q10MI9, Q1CW46, Q2HJB0, Q2IQ95, Q2RSY6, Q498J9, Q50863, Q50864, Q53JI9, Q53U11, Q566Q8, Q5GA22, Q5NAI7, Q6AYD1, Q72DW3, Q758T2, Q82JN8

Diamond homologs: A0AEZ6, A1ABR4, A1JKF8, A4TL15, A4W9L0, A5F1P8, A6M0L7, A6T7U7, A7FFP8, A7MTM7, A7ZMK0, A8A0S5, A8AHC4, A8MPS7, A9N261, A9R3W4, B0K272, B0KCX1, B1IPJ7, B1JR86, B1LDZ8, B1XGJ4, B2KA89, B4EZQ3, B4T4L5, B4TGF6, B4TUD7, B5BA58, B5F7H6, B5FJC2, B5QWH6, B5RAY7, B5XT26, B5YQ20, B6IBF3, B7HEK8, B7L6K7, B7LQ59, B7M1E5, B7MAU4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

452 predictions. Top by Δscore:

Variant	Effect	Δscore
22:21629303:CGCA:C	donor_loss	1.0000
22:21629305:CA:C	donor_loss	1.0000
22:21629845:CCTCA:C	donor_loss	1.0000
22:21629846:CTCA:C	donor_loss	1.0000
22:21629847:TCA:T	donor_loss	1.0000
22:21629848:CAC:C	donor_loss	1.0000
22:21629849:ACCT:A	donor_loss	1.0000
22:21628785:CAC:C	acceptor_gain	0.9900
22:21628789:T:A	acceptor_loss	0.9900
22:21629008:A:AC	donor_gain	0.9900
22:21629009:C:CC	donor_gain	0.9900
22:21629009:CCG:C	donor_gain	0.9900
22:21629183:CACGC:C	acceptor_gain	0.9900
22:21629185:CGC:C	acceptor_gain	0.9900
22:21629306:A:AC	donor_gain	0.9900
22:21629307:C:CC	donor_gain	0.9900
22:21629527:AACGG:A	donor_gain	0.9900
22:21628784:CCAC:C	acceptor_gain	0.9800
22:21628785:CACC:C	acceptor_gain	0.9800
22:21628788:C:CC	acceptor_gain	0.9800
22:21629002:AGCCT:A	donor_loss	0.9800
22:21629003:GCCTC:G	donor_loss	0.9800
22:21629004:CCTCA:C	donor_loss	0.9800
22:21629005:CTCAC:C	donor_loss	0.9800
22:21629006:TCA:T	donor_loss	0.9800
22:21629007:CAC:C	donor_loss	0.9800
22:21629008:ACCGC:A	donor_loss	0.9800
22:21629009:C:CT	donor_loss	0.9800
22:21629184:ACGC:A	acceptor_gain	0.9800
22:21629185:CGCC:C	acceptor_gain	0.9800

AlphaMissense

2043 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:21629739:G:C	H63D	0.996
22:21629974:T:A	D14V	0.996
22:21629973:G:C	D14E	0.995
22:21629973:G:T	D14E	0.995
22:21629977:T:A	D13V	0.995
22:21628657:G:C	H245D	0.994
22:21629731:G:C	N65K	0.994
22:21629731:G:T	N65K	0.994
22:21629739:G:T	H63N	0.994
22:21628598:G:C	F264L	0.993
22:21628598:G:T	F264L	0.993
22:21628600:A:G	F264L	0.993
22:21629332:G:C	H134D	0.993
22:21629975:C:G	D14H	0.993
22:21629330:G:C	H134Q	0.992
22:21629330:G:T	H134Q	0.992
22:21629726:G:A	S67F	0.992
22:21629968:C:T	G16D	0.992
22:21629976:G:C	D13E	0.992
22:21629976:G:T	D13E	0.992
22:21629978:C:G	D13H	0.992
22:21629324:G:C	H136Q	0.991
22:21629324:G:T	H136Q	0.991
22:21629974:T:G	D14A	0.991
22:21629334:C:T	G133E	0.990
22:21629737:G:C	H63Q	0.990
22:21629737:G:T	H63Q	0.990
22:21629974:T:C	D14G	0.988
22:21628655:G:C	H245Q	0.987
22:21628655:G:T	H245Q	0.987

dbSNP variants (sampled 300 via entrez): RS1000611225 (22:21631204 G>A), RS1001272449 (22:21630630 G>A), RS1001329710 (22:21630945 G>A,T), RS1002721986 (22:21628618 C>G,T), RS1003019962 (22:21629789 T>C,G), RS1003227772 (22:21628850 T>A), RS1003356378 (22:21628604 G>A), RS1003692173 (22:21628365 T>C), RS1004261822 (22:21629440 C>A,T), RS1004608531 (22:21630432 C>A,T), RS1004704704 (22:21630656 A>C), RS1005281906 (22:21628844 G>A,T), RS1007187870 (22:21627921 C>T), RS1007369512 (22:21627638 G>A), RS1008181924 (22:21631417 G>A)

Disease associations

OMIM: gene MIM:619770 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

23 associations (top):

Study	Trait	p-value
GCST000612_29	Celiac disease	2.000000e-07
GCST000879_5	Crohn’s disease	5.000000e-16
GCST001725_108	Inflammatory bowel disease	1.000000e-16
GCST001765_28	Red blood cell traits	9.000000e-10
GCST002318_165	Rheumatoid arthritis	2.000000e-07
GCST002318_36	Rheumatoid arthritis	2.000000e-09
GCST003155_25	Systemic lupus erythematosus	2.000000e-22
GCST003268_18	Psoriasis vulgaris	2.000000e-07
GCST004131_48	Inflammatory bowel disease	4.000000e-15
GCST004132_118	Crohn’s disease	1.000000e-15
GCST004133_48	Ulcerative colitis	9.000000e-06
GCST005523_39	Celiac disease	6.000000e-11
GCST005993_23	Mean corpuscular hemoglobin	3.000000e-10
GCST006051_3	Idiopathic inflammatory myopathy	5.000000e-07
GCST006959_181	Rheumatoid arthritis	4.000000e-06
GCST006959_79	Rheumatoid arthritis	6.000000e-07
GCST007278_26	Systemic seropositive rheumatic diseases (Systemic sclerosis or systemic lupus erythematosus or rheumatoid arthritis or idiopathic inflammatory myopathies)	1.000000e-13
GCST007827_18	Alzheimer’s disease or HDL levels (pleiotropy)	4.000000e-12
GCST009873_13	Autoimmune traits (pleiotropy)	2.000000e-08
GCST90002385_574	High light scatter reticulocyte count	3.000000e-26
GCST90002386_529	High light scatter reticulocyte percentage of red cells	6.000000e-29
GCST90002389_435	Lymphocyte percentage of white cells	2.000000e-33
GCST90002390_311	Mean corpuscular hemoglobin	7.000000e-44

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:1001494	psoriasis vulgaris
EFO:0004527	mean corpuscular hemoglobin
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0007986	reticulocyte count
EFO:0007993	lymphocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	3
bisphenol A	decreases expression, affects cotreatment	1
arsenite	affects binding, increases reaction	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
perfluoro-n-nonanoic acid	increases expression	1
2-palmitoylglycerol	increases expression	1
K 7174	decreases expression	1
NSC 689534	affects binding, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diuron	decreases expression	1
Doxorubicin	decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methotrexate	decreases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression, increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1
Antirheumatic Agents	decreases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3LG	Abcam HEK293T YDJC KO	Transformed cell line	Female

Clinical trials (associated diseases)

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