DPY19L4

dpy-19 like 4

Basic information

Region (hg38): 8:94719703-94793836

Links

ENSG00000156162 ∙ NCBI:286148 ∙ OMIM:613895 ∙ HGNC:27829 ∙ Uniprot:Q7Z388 ∙ 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 DPY19L4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPY19L4 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			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	27	2	1

Variants in DPY19L4

This is a list of pathogenic ClinVar variants found in the DPY19L4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-94720009-A-G		not specified	Uncertain significance (Sep 01, 2024)
8-94726333-C-A		not specified	Uncertain significance (Apr 04, 2024)
8-94726426-G-A		not specified	Uncertain significance (Jun 05, 2023)
8-94734665-G-A		not specified	Uncertain significance (Nov 22, 2023)
8-94734728-C-T		not specified	Uncertain significance (Oct 09, 2024)
8-94738431-T-A		not specified	Uncertain significance (Feb 06, 2024)
8-94739421-G-C		not specified	Uncertain significance (Nov 12, 2021)
8-94739460-A-G		not specified	Uncertain significance (Sep 30, 2024)
8-94739670-A-G		not specified	Uncertain significance (Dec 19, 2022)
8-94739739-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-94739757-G-A		not specified	Uncertain significance (Aug 07, 2024)
8-94739765-A-C		not specified	Uncertain significance (Jul 14, 2024)
8-94756047-C-T		not specified	Uncertain significance (Sep 06, 2022)
8-94756113-C-T		not specified	Uncertain significance (Oct 26, 2022)
8-94761814-T-C		not specified	Uncertain significance (Feb 01, 2023)
8-94765176-A-C			Likely benign (Nov 01, 2023)
8-94765241-T-G		not specified	Uncertain significance (Nov 11, 2024)
8-94765245-G-T		not specified	Uncertain significance (Nov 20, 2024)
8-94765261-G-T			Likely benign (Nov 01, 2023)
8-94765278-T-A		not specified	Uncertain significance (Sep 26, 2023)
8-94765775-G-A		not specified	Uncertain significance (Jun 10, 2024)
8-94768405-A-G		not specified	Uncertain significance (Apr 26, 2023)
8-94768430-C-A		not specified	Uncertain significance (Jun 07, 2023)
8-94768533-A-T		not specified	Uncertain significance (Apr 12, 2022)
8-94770478-C-G		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPY19L4	protein_coding	protein_coding	ENST00000414645	19	74134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.42e-21	0.0348	125276	0	471	125747	0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.573	337	368	0.916	0.0000177	4734
Missense in Polyphen		130	121.38	1.071		1667
Synonymous	1.65	103	127	0.814	0.00000616	1316
Loss of Function	1.15	37	45.3	0.816	0.00000252	558

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00280	0.00265
Ashkenazi Jewish	0.00873	0.00877
East Asian	0.00213	0.00212
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00156	0.00152
Middle Eastern	0.00213	0.00212
South Asian	0.00259	0.00255
Other	0.00247	0.00245

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0848

Intolerance Scores

• loftool: 0.980
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.71

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.174
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0145

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpy19l4

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