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.

• not_specified (76 variants)

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. These statistics are base on transcript: NM_001172774.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			73	3		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	73	3	0

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