DPY19L3

dpy-19 like C-mannosyltransferase 3

Basic information

Region (hg38): 19:32405543-32485895

Links

ENSG00000178904 ∙ NCBI:147991 ∙ OMIM:613894 ∙ HGNC:27120 ∙ Uniprot:Q6ZPD9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPY19L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPY19L3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	3	0

Variants in DPY19L3

This is a list of pathogenic ClinVar variants found in the DPY19L3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-32408263-A-C		not specified	Uncertain significance (Jun 09, 2022)
19-32408332-A-G		not specified	Uncertain significance (Mar 02, 2023)
19-32411295-G-T		not specified	Uncertain significance (Sep 01, 2021)
19-32432800-G-A		not specified	Likely benign (Oct 17, 2023)
19-32437261-C-G		not specified	Uncertain significance (May 17, 2023)
19-32437281-C-G		not specified	Uncertain significance (Apr 08, 2024)
19-32439168-C-G		not specified	Uncertain significance (Dec 15, 2022)
19-32439210-G-C		not specified	Uncertain significance (Jun 30, 2022)
19-32439893-A-G		not specified	Uncertain significance (Dec 03, 2021)
19-32453193-A-G		not specified	Uncertain significance (Nov 17, 2022)
19-32453238-A-G		not specified	Uncertain significance (Sep 26, 2023)
19-32454958-G-A		not specified	Likely benign (May 11, 2022)
19-32454967-A-G		not specified	Uncertain significance (Oct 12, 2022)
19-32455000-T-C		not specified	Uncertain significance (Jan 08, 2024)
19-32455020-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-32455032-A-G		not specified	Uncertain significance (Nov 08, 2022)
19-32458116-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-32458352-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-32458470-C-T		not specified	Uncertain significance (May 08, 2024)
19-32458485-T-G		not specified	Uncertain significance (Dec 13, 2022)
19-32458505-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-32463385-T-C		not specified	Uncertain significance (Aug 17, 2021)
19-32463433-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-32463447-A-G		not specified	Uncertain significance (Sep 13, 2023)
19-32464779-T-C		not specified	Uncertain significance (Jun 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPY19L3	protein_coding	protein_coding	ENST00000342179	18	80353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.85e-7	1.00	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	292	384	0.760	0.0000199	4672
Missense in Polyphen		74	140.28	0.5275		1709
Synonymous	-0.807	160	148	1.08	0.00000801	1376
Loss of Function	3.29	18	40.6	0.443	0.00000206	499

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000594	0.000594
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000218	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000364	0.000360
Middle Eastern	0.000218	0.000217
South Asian	0.000263	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable C-mannosyltransferase that mediates C- mannosylation of tryptophan residues on target proteins. {ECO:0000250}.

Recessive Scores

• pRec: 0.0658

Intolerance Scores

• loftool: 0.810
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.91

Haploinsufficiency Scores

• pHI: 0.0902
• hipred: N
• hipred_score: 0.476
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dpy19l3
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan
• Cellular component: nuclear inner membrane;integral component of membrane
• Molecular function: mannosyltransferase activity