DPY19L1

Summary

DPY19L1 (dpy-19 like C-mannosyltransferase 1, HGNC:22205) is a protein-coding gene on chromosome 7p14.2, encoding Protein C-mannosyl-transferase DPY19L1 (Q2PZI1). C-mannosyltransferase that mediates the C-mannosylation tryptophan residues on target proteins.

Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Located in membrane.

Source: NCBI Gene 23333 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 106 total — 1 likely-pathogenic
• MANE Select transcript: NM_001366673

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22205
Approved symbol	DPY19L1
Name	dpy-19 like C-mannosyltransferase 1
Location	7p14.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0877
Ensembl gene	ENSG00000173852
Ensembl biotype	protein_coding
OMIM	613892
Entrez	23333

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 14 protein_coding, 3 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000310974, ENST00000428054, ENST00000446375, ENST00000462134, ENST00000463538, ENST00000481923, ENST00000493989, ENST00000612226, ENST00000638088, ENST00000685246, ENST00000687726, ENST00000688296, ENST00000690503, ENST00000690666, ENST00000928159, ENST00000928160, ENST00000944845, ENST00000944846, ENST00000944847, ENST00000944848, ENST00000944849

RefSeq mRNA: 2 — MANE Select: NM_001366673 NM_001366673, NM_015283

CCDS: CCDS43567, CCDS94084

Canonical transcript exons

ENST00000638088 — 22 exons

Exon	Start	End
ENSE00001505374	34940153	34940327
ENSE00001595454	34957984	34958070
ENSE00001604724	34949797	34949898
ENSE00001637040	34945667	34945716
ENSE00001670900	34937994	34938119
ENSE00001673521	34939276	34939375
ENSE00001696554	34954698	34954778
ENSE00001738698	34941765	34941884
ENSE00001763524	34942615	34942639
ENSE00001786648	34947630	34947701
ENSE00003499655	34955308	34955367
ENSE00003544259	34989884	34989941
ENSE00003552036	35011330	35011450
ENSE00003571041	34969433	34969532
ENSE00003576616	35018572	35018596
ENSE00003579441	35010468	35010561
ENSE00003631844	35017882	35017969
ENSE00003656737	34973514	34973605
ENSE00003690513	34966894	34966971
ENSE00003690775	35013568	35013705
ENSE00003796188	35037097	35037485
ENSE00003900268	34928881	34931729

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 96.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.5912 / max 244.9347, expressed in 1805 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
83531	28.0486	1805
83529	0.6909	364
83530	0.6162	350
83532	0.1224	42
83533	0.1131	24

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	96.56	gold quality
pons	UBERON:0000988	95.03	gold quality
stromal cell of endometrium	CL:0002255	93.60	gold quality
right testis	UBERON:0004534	93.58	gold quality
left testis	UBERON:0004533	93.54	gold quality
spinal cord	UBERON:0002240	92.59	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.57	gold quality
ventricular zone	UBERON:0003053	92.44	gold quality
sperm	CL:0000019	92.27	gold quality
testis	UBERON:0000473	92.18	gold quality
choroid plexus epithelium	UBERON:0003911	91.85	gold quality
inferior vagus X ganglion	UBERON:0005363	90.96	gold quality
male germ cell	CL:0000015	90.73	gold quality
medulla oblongata	UBERON:0001896	90.62	gold quality
embryo	UBERON:0000922	90.30	gold quality
inferior olivary complex	UBERON:0002127	90.26	gold quality
germinal epithelium of ovary	UBERON:0001304	90.19	gold quality
subthalamic nucleus	UBERON:0001906	90.19	gold quality
cerebellar vermis	UBERON:0004720	89.61	gold quality
superior vestibular nucleus	UBERON:0007227	89.56	gold quality
corpus callosum	UBERON:0002336	89.43	gold quality
adrenal tissue	UBERON:0018303	89.28	gold quality
prefrontal cortex	UBERON:0000451	89.00	gold quality
cartilage tissue	UBERON:0002418	88.61	gold quality
endometrium	UBERON:0001295	88.43	gold quality
Brodmann (1909) area 10	UBERON:0013541	88.40	gold quality
smooth muscle tissue	UBERON:0001135	88.28	gold quality
calcaneal tendon	UBERON:0003701	87.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.84	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.72

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	dpy19l1l	ENSDARG00000069995
mus_musculus	Dpy19l1	ENSMUSG00000043067
rattus_norvegicus	Dpy19l1	ENSRNOG00000026589
caenorhabditis_elegans		WBGENE00001078

Paralogs (3): DPY19L4 (ENSG00000156162), DPY19L2 (ENSG00000177990), DPY19L3 (ENSG00000178904)

Protein

Protein identifiers

Protein C-mannosyl-transferase DPY19L1 — Q2PZI1 (reviewed: Q2PZI1)

Alternative names: Dpy-19-like protein 1, Protein dpy-19 homolog 1

All UniProt accessions (8): Q2PZI1, A0A1B0GW05, A0A8I5KPK9, A0A8I5KSD1, A0A8I5KUQ5, A0A8J9BZN9, H7C1I8, H7C3M5

UniProt curated annotations — full annotation on UniProt →

Function. C-mannosyltransferase that mediates the C-mannosylation tryptophan residues on target proteins. The reaction occurs on the luminal side of the endoplasmic reticulum and involves the transfer of a mannose unit from a dolichylphosphate mannose (Dol-P-Man) donor to an acceptor protein containing a WxxW consensus sequence. C-mannosylates the first two tryptophans in the WxxWxxWxxC motif in thrombospondin (TSP) type-1 of UNC5A. Regulates neurite extension during development.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the dpy-19 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q2PZI1-1	1	yes
Q2PZI1-2	2

RefSeq proteins (2): NP_001353602, NP_056098 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018732	Dpy-19/Dpy-19-like	Family
IPR047463	Dpy19L1	Family

Pfam: PF10034

Catalyzed reactions (Rhea), 1 shown:

• L-tryptophyl-[protein] + a di-trans,poly-cis-dolichyl beta-D-mannosyl phosphate = C-alpha-D-mannosyl-L-tryptophyl-[protein] + a di-trans,poly-cis-dolichyl phosphate + H(+) (RHEA:77219)

UniProt features (15 total): transmembrane region 11, chain 1, region of interest 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2PZI1-F1	88.51	0.65

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 207 (showing top): HORIUCHI_WTAP_TARGETS_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, YAGI_AML_WITH_INV_16_TRANSLOCATION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN, KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP, BILD_E2F3_ONCOGENIC_SIGNATURE, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, SENESE_HDAC1_TARGETS_UP, CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN, GRADE_COLON_AND_RECTAL_CANCER_UP, YAGI_AML_WITH_11Q23_REARRANGED, SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP

GO Biological Process (2): obsolete protein glycosylation (GO:0006486), protein C-linked glycosylation (GO:0018103)

GO Molecular Function (3): mannosyltransferase activity (GO:0000030), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), endoplasmic reticulum (GO:0005783)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycoprotein biosynthetic process	1
hexosyltransferase activity	1
catalytic activity	1
transferase activity	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

642 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DPY19L1	EFCAB11	Q9BUY7	589
DPY19L1	TSR3	Q9UJK0	540
DPY19L1	NPSR1	Q6W5P4	503
DPY19L1	MANBAL	Q9NQG1	490
DPY19L1	TSR1	Q2NL82	462
DPY19L1	TSR2	Q969E8	460
DPY19L1	OR5I1	Q13606	448
DPY19L1	UNC5A	Q6ZN44	446
DPY19L1	FAM24A	A6NFZ4	431
DPY19L1	ADAMTSL1	Q8N6G6	427
DPY19L1	CCDC152	Q4G0S7	397
DPY19L1	SYNDIG1	Q9H7V2	379
DPY19L1	NT5DC1	Q5TFE4	370
DPY19L1	ZNF616	Q08AN1	360
DPY19L1	STT3A	P46977	355

IntAct

105 interactions, top by confidence:

A	B	Type	Score
LDLRAD4	NEDD4	psi-mi:“MI:0914”(association)	0.690
BTN3A3	BTN3A1	psi-mi:“MI:0914”(association)	0.560
SEMA7A	SGPL1	psi-mi:“MI:0914”(association)	0.530
APLNR	METTL15	psi-mi:“MI:0914”(association)	0.530
CDRT15	CDRT15L2	psi-mi:“MI:0914”(association)	0.530
SCN3B	ABCC5	psi-mi:“MI:0914”(association)	0.530
TNFRSF8	DAPK3	psi-mi:“MI:0914”(association)	0.530
TCTN2	TPST2	psi-mi:“MI:0914”(association)	0.530
THBS2	AP1G2	psi-mi:“MI:0914”(association)	0.530
SCNN1D	ABHD16A	psi-mi:“MI:0914”(association)	0.530
	UBXN8	psi-mi:“MI:0914”(association)	0.530
SLC22A9	GPR89A	psi-mi:“MI:0914”(association)	0.530
LDLRAD4	WWP2	psi-mi:“MI:0914”(association)	0.530
PBXIP1	GOLIM4	psi-mi:“MI:0914”(association)	0.530
HEATR3	SLC27A2	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
TMEM184A	SLC33A1	psi-mi:“MI:0914”(association)	0.530
PBXIP1	KCNN4	psi-mi:“MI:0914”(association)	0.530
ANKRD22	ESYT2	psi-mi:“MI:0914”(association)	0.530

BioGRID (115): DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Proximity Label-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS), DPY19L1 (Affinity Capture-MS)

ESM2 similar proteins: A0A078H868, A0AAS4, A0JP80, A6X919, D4AD75, O70536, O77760, O77761, P23913, P35610, P53439, P56079, Q14739, Q20696, Q20735, Q28677, Q2PZI1, Q4JM44, Q4R763, Q5R7H4, Q5RK27, Q60457, Q61263, Q63632, Q63633, Q657W3, Q6AX73, Q6Z0E2, Q7T3T4, Q7TSX5, Q86VZ5, Q8IWX5, Q8NHU3, Q8VCQ6, Q91V14, Q924N4, Q965Q4, Q9D4B1, Q9FJB4, Q9H2X9

Diamond homologs: A6X919, A8Y3M2, D4AD75, P0CW70, P34413, Q2PZI1, Q5RCJ4, Q6NUT2, Q6NXN4, Q6ZN68, Q6ZPD9, Q71B07, A2AJQ3, Q5R8N9, Q7Z388, Q9VWR8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	78
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3062981	GRCh37/hg19 7p14.3-14.1(chr7:33478398-39686397)x1	Likely pathogenic

SpliceAI

3286 predictions. Top by Δscore:

Variant	Effect	Δscore
7:34931725:CAGGC:C	acceptor_gain	1.0000
7:34931727:GGC:G	acceptor_gain	1.0000
7:34931730:C:CC	acceptor_gain	1.0000
7:34931730:CTA:C	acceptor_loss	1.0000
7:34946012:TGAA:T	donor_gain	1.0000
7:34954696:A:AC	donor_gain	1.0000
7:34954697:C:CC	donor_gain	1.0000
7:34954697:CGT:C	donor_gain	1.0000
7:34989937:TGCCA:T	acceptor_gain	1.0000
7:34989939:CCA:C	acceptor_gain	1.0000
7:34989940:CA:C	acceptor_gain	1.0000
7:34989940:CAC:C	acceptor_gain	1.0000
7:34989941:ACT:A	acceptor_loss	1.0000
7:34989942:C:CA	acceptor_loss	1.0000
7:34989942:C:CC	acceptor_gain	1.0000
7:35011325:CTTA:C	donor_loss	1.0000
7:35011326:TTAC:T	donor_loss	1.0000
7:35011327:TA:T	donor_loss	1.0000
7:35011328:A:AC	donor_gain	1.0000
7:35011328:AC:A	donor_gain	1.0000
7:35011328:ACCTT:A	donor_gain	1.0000
7:35011329:C:CC	donor_gain	1.0000
7:35011329:CC:C	donor_gain	1.0000
7:35011329:CCT:C	donor_gain	1.0000
7:35011329:CCTT:C	donor_gain	1.0000
7:35011329:CCTTC:C	donor_gain	1.0000
7:35011446:ATTAC:A	acceptor_gain	1.0000
7:35011447:TTAC:T	acceptor_gain	1.0000
7:35011448:TAC:T	acceptor_gain	1.0000
7:35011448:TACC:T	acceptor_loss	1.0000

AlphaMissense

4867 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:34941826:C:G	R470T	1.000
7:34949815:A:C	F395L	1.000
7:34949815:A:T	F395L	1.000
7:34949817:A:G	F395L	1.000
7:34949828:C:T	C391Y	1.000
7:34969465:A:G	W255R	1.000
7:34969465:A:T	W255R	1.000
7:34973567:G:C	S214R	1.000
7:34973567:G:T	S214R	1.000
7:34973569:T:G	S214R	1.000
7:34931661:C:G	C647S	0.999
7:34931662:A:G	C647R	0.999
7:34931662:A:T	C647S	0.999
7:34931721:C:G	C627S	0.999
7:34931722:A:T	C627S	0.999
7:34938119:T:A	R582S	0.999
7:34938119:T:G	R582S	0.999
7:34939276:C:G	R582T	0.999
7:34939291:T:A	E577V	0.999
7:34939300:G:T	P574Q	0.999
7:34939303:T:C	H573R	0.999
7:34939305:A:C	N572K	0.999
7:34939305:A:T	N572K	0.999
7:34939330:A:G	L564P	0.999
7:34939363:G:T	A553E	0.999
7:34940185:A:G	L538P	0.999
7:34940208:G:C	F530L	0.999
7:34940208:G:T	F530L	0.999
7:34940210:A:G	F530L	0.999
7:34941819:T:A	K472N	0.999

dbSNP variants (sampled 300 via entrez): RS1000018393 (7:35019821 T>C), RS1000069848 (7:34940565 C>T), RS1000070745 (7:35019527 A>G), RS1000085979 (7:35025639 T>C), RS1000106047 (7:35002709 G>T), RS1000166094 (7:34946278 C>T), RS1000256107 (7:34992403 TGA>T), RS1000362887 (7:34934279 T>A), RS1000399141 (7:34951935 C>T), RS1000508396 (7:34998310 GGGA>G), RS1000536185 (7:34980691 T>G), RS1000540151 (7:35037248 G>C), RS1000655144 (7:34964352 C>T), RS1000671388 (7:35009899 T>C), RS1000671968 (7:34945860 A>T)

Disease associations

OMIM: gene MIM:613892 | disease phenotypes: MIM:109730

GenCC curated gene-disease

Mondo (1): aortic valve disease 1 (MONDO:0024523)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST003262_389	Post bronchodilator FEV1	4.000000e-06
GCST003262_390	Post bronchodilator FEV1	5.000000e-06
GCST006098_6	Vigorous physical activity	6.000000e-10
GCST006857_1	Leisure-time exercise behaviour	2.000000e-09
GCST010136_11	Fruit consumption	1.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004314	forced expiratory volume
EFO:0008002	physical activity measurement
EFO:0000483	exercise
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, decreases methylation	6
trichostatin A	increases expression, affects cotreatment	2
Vorinostat	affects cotreatment, increases expression	2
Cisplatin	decreases expression, increases expression	2
aristolochic acid I	decreases expression	1
bisphenol F	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
butyraldehyde	decreases expression	1
ochratoxin A	increases expression	1
di-n-butylphosphoric acid	affects expression	1
pentabromodiphenyl ether	decreases expression	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment, increases expression	1
bisphenol B	increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	decreases expression, affects cotreatment, increases expression	1
jinfukang	decreases expression	1
bisphenol AF	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Bilirubin	decreases expression	1
Cadmium	increases expression, increases abundance	1
Calcitriol	increases expression	1
Coumestrol	increases expression	1
Fluorouracil	affects response to substance	1
Formaldehyde	decreases expression	1
Ivermectin	decreases expression	1
Nickel	increases expression	1

Clinical trials (associated diseases)

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