DPY19L1

dpy-19 like C-mannosyltransferase 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 7:34927292-35038271

Links

ENSG00000173852 ∙ NCBI:23333 ∙ OMIM:613892 ∙ HGNC:22205 ∙ Uniprot:Q2PZI1 ∙ 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 DPY19L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPY19L1 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	0

Variants in DPY19L1

This is a list of pathogenic ClinVar variants found in the DPY19L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-34931605-C-T		not specified	Uncertain significance (Sep 16, 2021)
7-34931672-T-G		not specified	Uncertain significance (Aug 28, 2024)
7-34931682-T-C		not specified	Uncertain significance (Mar 02, 2023)
7-34938000-C-A		not specified	Uncertain significance (Oct 29, 2021)
7-34938055-G-C		not specified	Uncertain significance (Jan 30, 2024)
7-34938060-C-T		not specified	Likely benign (Apr 12, 2022)
7-34938084-C-T		not specified	Uncertain significance (Sep 25, 2023)
7-34938106-T-C		not specified	Uncertain significance (May 23, 2023)
7-34939282-C-G		not specified	Uncertain significance (Dec 06, 2021)
7-34940199-C-A		not specified	Uncertain significance (Jul 25, 2023)
7-34940219-C-T		not specified	Uncertain significance (Mar 23, 2023)
7-34940224-T-C		not specified	Uncertain significance (Jul 19, 2023)
7-34940254-T-G		not specified	Uncertain significance (Apr 19, 2024)
7-34940284-A-G		not specified	Uncertain significance (Mar 29, 2023)
7-34940327-G-C		not specified	Uncertain significance (Oct 08, 2024)
7-34941828-C-T		not specified	Uncertain significance (Apr 23, 2024)
7-34947647-C-T		not specified	Likely benign (Oct 26, 2024)
7-34947662-C-T		not specified	Uncertain significance (Jun 13, 2023)
7-34947671-G-A		not specified	Uncertain significance (Oct 11, 2024)
7-34955310-A-G		not specified	Uncertain significance (Jul 25, 2023)
7-34955339-A-G		not specified	Uncertain significance (Aug 10, 2021)
7-34958004-A-C		not specified	Uncertain significance (Dec 27, 2023)
7-34958006-G-A		not specified	Uncertain significance (May 05, 2023)
7-34958028-T-C		not specified	Uncertain significance (Aug 12, 2021)
7-34966896-T-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPY19L1	protein_coding	protein_coding	ENST00000310974	22	109396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000132	1.00	125182	0	20	125202	0.0000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	246	315	0.781	0.0000150	4373
Missense in Polyphen		57	112.98	0.50451		1559
Synonymous	0.537	99	106	0.934	0.00000516	1244
Loss of Function	3.75	14	39.4	0.355	0.00000190	545

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000286
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000656	0.0000617
Middle Eastern	0.000111	0.000109
South Asian	0.000120	0.0000980
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}.

Intolerance Scores

• loftool: 0.530
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.443
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.346

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpy19l1

Gene ontology

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