C1GALT1C1L

Summary

C1GALT1C1L (C1GALT1 specific chaperone 1 like, HGNC:51617) is a protein-coding gene on chromosome 2p21, encoding C1GALT1-specific chaperone 1-like protein (P0DN25).

Predicted to enable glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity. Predicted to be located in membrane.

Source: NCBI Gene 728819 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_001101330

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51617
Approved symbol	C1GALT1C1L
Name	C1GALT1 specific chaperone 1 like
Location	2p21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000223658
Ensembl biotype	protein_coding
Entrez	728819

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000475092

RefSeq mRNA: 1 — MANE Select: NM_001101330 NM_001101330

CCDS: CCDS82442

Canonical transcript exons

ENST00000475092 — 1 exons

Exon	Start	End
ENSE00001862661	43675151	43676429

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 86.48.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5788 / max 13.6086, expressed in 335 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
28099	0.5167	315
28098	0.0621	27

Top tissues by expression

249 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	86.48	gold quality
calcaneal tendon	UBERON:0003701	76.17	gold quality
smooth muscle tissue	UBERON:0001135	73.46	gold quality
islet of Langerhans	UBERON:0000006	71.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	70.77	gold quality
body of uterus	UBERON:0009853	70.39	gold quality
right testis	UBERON:0004534	69.51	gold quality
left testis	UBERON:0004533	69.21	gold quality
testis	UBERON:0000473	69.08	gold quality
kidney epithelium	UBERON:0004819	68.93	gold quality
decidua	UBERON:0002450	68.42	gold quality
right adrenal gland cortex	UBERON:0035827	68.11	gold quality
tibia	UBERON:0000979	67.90	gold quality
right adrenal gland	UBERON:0001233	67.25	gold quality
left adrenal gland	UBERON:0001234	67.21	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	67.17	gold quality
muscle layer of sigmoid colon	UBERON:0035805	66.93	gold quality
left adrenal gland cortex	UBERON:0035825	66.78	gold quality
endometrium	UBERON:0001295	66.60	gold quality
cardiac muscle of right atrium	UBERON:0003379	66.41	gold quality
right atrium auricular region	UBERON:0006631	66.10	gold quality
uterus	UBERON:0000995	66.00	gold quality
left ventricle myocardium	UBERON:0006566	65.90	gold quality
cardiac atrium	UBERON:0002081	65.61	gold quality
adrenal cortex	UBERON:0001235	65.41	gold quality
descending thoracic aorta	UBERON:0002345	65.08	gold quality
corpus epididymis	UBERON:0004359	65.05	gold quality
pigmented layer of retina	UBERON:0001782	64.92	gold quality
left coronary artery	UBERON:0001626	64.87	gold quality
myometrium	UBERON:0001296	64.66	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting C1GALT1C1L, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-449B-3P	99.20	67.24	1047
HSA-MIR-4520-2-3P	99.14	69.28	1009
HSA-MIR-361-5P	98.95	70.16	1340
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-633	98.35	69.45	1167
HSA-MIR-5585-5P	97.95	68.80	1024
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-4309	97.84	65.45	588
HSA-MIR-3198	97.84	65.64	579
HSA-MIR-7847-3P	96.63	64.58	952

Cross-species orthologs

13 orthologs

Organism	Symbol	Gene ID
danio_rerio	c1galt1c1	ENSDARG00000036335
drosophila_melanogaster	tgy	FBGN0030984
drosophila_melanogaster	CG18558	FBGN0031469
drosophila_melanogaster	CG2983	FBGN0031472
drosophila_melanogaster	CG34057	FBGN0054057
caenorhabditis_elegans	E03H4.3	WBGENE00008471
caenorhabditis_elegans	F56H6.1	WBGENE00010162
caenorhabditis_elegans		WBGENE00015361
caenorhabditis_elegans		WBGENE00015861
caenorhabditis_elegans		WBGENE00015871
caenorhabditis_elegans		WBGENE00021403
caenorhabditis_elegans		WBGENE00021407
caenorhabditis_elegans		WBGENE00044620

Paralogs (2): C1GALT1 (ENSG00000106392), C1GALT1C1 (ENSG00000171155)

Protein

Protein identifiers

C1GALT1-specific chaperone 1-like protein — P0DN25 (reviewed: P0DN25)

All UniProt accessions (1): P0DN25

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the glycosyltransferase 31 family. Beta3-Gal-T subfamily.

RefSeq proteins (1): NP_001094800* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026050	C1GALT1/C1GALT1_chp1	Family

UniProt features (6 total): topological domain 2, glycosylation site 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DN25-F1	84.47	0.53

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): 55, 301

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, GOBP_GLYCOPROTEIN_BIOSYNTHETIC_PROCESS, MIR1468_3P, MIR576_5P, MIR12132, MIR633, MIR5585_5P, DESCARTES_MAIN_FETAL_CCL19_CCL21_POSITIVE_CELLS, DESCARTES_FETAL_PANCREAS_CCL19_CCL21_POSITIVE_CELLS, ZSCAN5DP_TARGET_GENES, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_4H_ACT_CD4_TCELL_UP, GSE29615_CTRL_VS_DAY7_LAIV_FLU_VACCINE_PBMC_DN

GO Biological Process (1): protein O-linked glycosylation (GO:0006493)

GO Molecular Function (1): N-acetylgalactosaminide beta-1,3-galactosyltransferase activity (GO:0016263)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycoprotein biosynthetic process	1
UDP-galactosyltransferase activity	1
beta-1,3-galactosyltransferase activity	1
catalytic activity, acting on a glycoprotein	1
cellular anatomical structure	1

Protein interactions and networks

STRING

218 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
C1GALT1C1L	DCAF10	Q5QP82	555
C1GALT1C1L	ZNF182	P17025	443
C1GALT1C1L	B3GNT2	Q9NY97	405
C1GALT1C1L	B3GNT6	Q6ZMB0	403
C1GALT1C1L	FAM177A1	Q8N128	392
C1GALT1C1L	GALNT11	Q8NCW6	391
C1GALT1C1L	GALNT12	Q8IXK2	370
C1GALT1C1L	GALNT4	Q8N4A0	348
C1GALT1C1L	SRM	P19623	347
C1GALT1C1L	B3GALT4	O96024	325
C1GALT1C1L	ABO	P16442	325
C1GALT1C1L	RMND5A	Q9H871	323
C1GALT1C1L	B4GALT2	O60909	316
C1GALT1C1L	ATP6V1G3	Q96LB4	315
C1GALT1C1L	THSD1	Q9NS62	310

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SLC22A23	NRP1	psi-mi:“MI:0914”(association)	0.350

ESM2 similar proteins: A0A2C9JXL4, E9Q649, O95395, P0DN25, P97402, Q08BL3, Q0VC84, Q18515, Q24342, Q3SX46, Q499P3, Q5F3G7, Q5HZL5, Q5U258, Q5XJP0, Q5YB40, Q66GS2, Q6A1G2, Q6DE15, Q6DJR8, Q6GNL1, Q6P3P5, Q6P6V1, Q6WV16, Q6Y288, Q7K237, Q7SYI5, Q7T3S5, Q7Z1Z1, Q864U8, Q866Z5, Q8BGY6, Q8BHT6, Q8L7M1, Q8LPF8, Q8N0V5, Q8NCW6, Q96EU7, Q99NB2, Q9BYG0

Diamond homologs: P0DN25, Q3SX46, Q499P3, Q96EU7, Q9JMG2, Q08BL3, Q18515, Q5F3G7, Q7K237, Q9JJ05

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

172 predictions. Top by Δscore:

Variant	Effect	Δscore
2:43675472:T:TA	donor_gain	0.7700
2:43675514:T:C	donor_gain	0.7500
2:43675473:C:A	donor_gain	0.7400
2:43675848:T:C	acceptor_gain	0.7300
2:43675846:CCT:C	acceptor_gain	0.7100
2:43675462:CATCA:C	donor_gain	0.6600
2:43675469:A:AC	donor_gain	0.6600
2:43675470:C:CC	donor_gain	0.6600
2:43675614:AAT:A	donor_gain	0.6600
2:43675539:G:A	donor_gain	0.6400
2:43675471:T:C	donor_gain	0.6300
2:43675845:CCCT:C	acceptor_gain	0.6300
2:43675533:C:CT	donor_gain	0.6100
2:43675534:T:TT	donor_gain	0.6100
2:43675559:G:A	donor_gain	0.6100
2:43675599:CAT:C	donor_gain	0.6000
2:43675606:T:TA	donor_gain	0.6000
2:43675607:C:A	donor_gain	0.6000
2:43675610:T:TA	donor_gain	0.6000
2:43675537:T:C	donor_gain	0.5900
2:43675539:G:GC	donor_gain	0.5900
2:43675540:C:CC	donor_gain	0.5900
2:43675466:A:AC	donor_gain	0.5800
2:43675531:TAC:T	donor_gain	0.5800
2:43675595:A:C	donor_gain	0.5800
2:43675599:CATCT:C	donor_gain	0.5800
2:43675303:CA:C	donor_gain	0.5600
2:43675600:A:C	donor_gain	0.5600
2:43675532:A:AC	donor_gain	0.5400
2:43675535:A:AC	donor_gain	0.5400

AlphaMissense

2112 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:43675594:A:C	F243L	0.954
2:43675594:A:T	F243L	0.954
2:43675596:A:G	F243L	0.954
2:43675885:A:C	F146L	0.939
2:43675885:A:T	F146L	0.939
2:43675887:A:G	F146L	0.939
2:43675498:G:C	F275L	0.936
2:43675498:G:T	F275L	0.936
2:43675500:A:G	F275L	0.936
2:43675435:A:C	F296L	0.920
2:43675435:A:T	F296L	0.920
2:43675437:A:G	F296L	0.920
2:43675909:G:C	F138L	0.911
2:43675909:G:T	F138L	0.911
2:43675911:A:G	F138L	0.911
2:43675759:G:C	S188R	0.909
2:43675759:G:T	S188R	0.909
2:43675761:T:G	S188R	0.909
2:43675405:G:C	F306L	0.893
2:43675405:G:T	F306L	0.893
2:43675407:A:G	F306L	0.893
2:43676050:C:A	W91C	0.891
2:43676050:C:G	W91C	0.891
2:43675972:C:A	W117C	0.882
2:43675972:C:G	W117C	0.882
2:43675874:T:A	E150V	0.878
2:43675914:A:G	W137R	0.873
2:43675914:A:T	W137R	0.873
2:43675864:C:A	K153N	0.857
2:43675864:C:G	K153N	0.857

dbSNP variants (sampled 300 via entrez): RS1000260337 (2:43676807 T>C), RS1000981254 (2:43677229 T>C), RS1001357607 (2:43677297 A>G), RS1002984317 (2:43674851 G>A), RS1006457476 (2:43674916 C>A,G,T), RS1006903956 (2:43676713 T>G), RS1006929892 (2:43675811 A>G), RS1007020010 (2:43676936 A>G), RS1007641754 (2:43678304 G>C), RS1008018253 (2:43678148 G>A,T), RS1009202558 (2:43677979 C>T), RS1009744359 (2:43678194 C>A,T), RS1010128749 (2:43676998 C>T), RS1012148646 (2:43674667 C>A), RS1012240787 (2:43677651 C>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
dicrotophos	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
Leflunomide	decreases expression	1
Cisplatin	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Vanadates	decreases expression	1

Clinical trials (associated diseases)

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